Dear Dr Stakos, after Dr Hatzis has clarified the conditions for the additional analysis, which I assume you agree with, I have processed your data with all paired samples treated as such. While the unpaired analysis provided a total of 6 significantly differentially expressed genes (DEGs) in all 16 contrasts, the paired analysis provides 24. In the table below you find the number of sig. DEGs in each contrast. Down Up Contrast_result_filename 0 0 edgeRgenes_AvsB_UntrPMN_vs_PMNsIRAplasma_paired_featurecountExpr.csv 1 0 edgeRgenes_AvsC_UntrPMN_vs_PMNsIRAplasmaTIC_paired_featurecountExpr.csv 6 1 edgeRgenes_AvsD_UntrPMN_vs_PMNsIRAplasmaIL29_paired_featurecountExpr.csv 0 0 edgeRgenes_BvsC_PMNsIRAplasma_vs_PMNsIRAplasmaTIC_paired_featurecountExpr.csv 0 0 edgeRgenes_BvsD_PMNsIRAplasma_vs_PMNsIRAplasmaIL29_paired_featurecountExpr.csv 0 8 edgeRgenes_EvsF_UntrPMNs_vs_PMNspolyP_paired_featurecountExpr.csv 0 2 edgeRgenes_EvsG_UntrPMNs_vs_PMNspolyPTIC_paired_featurecountExpr.csv 0 0 edgeRgenes_EvsH_UntrPMNs_vs_PMNspolyPIL29_paired_featurecountExpr.csv 0 0 edgeRgenes_EvsI_UntrPMNs_vs_PMNsTIC_paired_featurecountExpr.csv 0 1 edgeRgenes_EvsJ_UntrPMNs_vs_PMNsIL29_paired_featurecountExpr.csv 0 0 edgeRgenes_FvsG_PMNspolyP_vs_PMNspolyPTIC_paired_featurecountExpr.csv 2 1 edgeRgenes_FvsH_PMNspolyP_vs_PMNspolyPIL29_paired_featurecountExpr.csv 0 0 edgeRgenes_FvsI_PMNspolyP_vs_PMNsTIC_paired_featurecountExpr.csv 0 0 edgeRgenes_FvsJ_PMNspolyP_vs_PMNsIL29_paired_featurecountExpr.csv 1 1 edgeRgenes_GvsI_PMNspolyPTIC_vs_PMNsTIC_paired_featurecountExpr.csv 0 0 edgeRgenes_GvsJ_PMNspolyPTIC_vs_PMNsIL29_paired_featurecountExpr.csv 10 14 total You can find these files at http://genomics-lab.fleming.gr/fleming/external/DrStakos/run409/paired/ The format of each file is: genes Ensembl gene ID logFC estimate of the log2-fold-change corresponding to the effect or contrast AveExpr average log2-expression for the probe over all samples F moderated F-statistic PValue raw p-value FDR adjusted p-value or q-value gene_name human readable gene name biotype gene biotype (PCG, lincRNA, ...) [sampleID] normalized counts for each sample DEG were assessed using the Bioconductor EdgeR package described in: McCarthy DJ, Chen Y, Smyth GK (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), 4288-4297. doi:10.1093/nar/gks042. Note that in EdgeR for a comparison A_vs_B, B is the reference condition. This is the usual arrangement, but opposite to the previous results produced with metaseqR. Let me know if you need further information. Best regards Martin -- Dr. Martin Reczko Staff research scientist professor level Institute for Fundamental Biomedical Science Biomedical Sciences Research Center "Alexander Fleming" Technical Coordinator - ELIXIR Greece 34 Fleming Street 16672 Vari, Greece Tel. +30-210-9656310 (ext. 144) FAX: +30-210-9653934 email: reczko@fleming.gr the analysis of your RNAseq experiment has finished. At http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=hg19&hubUrl=http://genomics-lab.fleming.gr/fleming/external/DrStakos/run409/hub.txt you will find tracks for all samples integrated for the UCSC genome browser. These tracks are sampled to smallest library (DSt3R7-3C-PMNsIRAplasmaTIC with 2853922 reads). sample n_reads DSt3R1-1A-UntrPMNs 4773312 DSt3R2-1B-PMNsIRAplasma 12401089 DSt3R3-1C-PMNsIRAplasmaTIC 8711500 DSt3R4-1D-PMNsIRAplasmaIL29 6595993 DSt3R5-3A-UntrPMNs 3669797 DSt3R6-3B-PMNsIRAplasma 7317844 DSt3R7-3C-PMNsIRAplasmaTIC 2853922 DSt3R8-3D-PMNsIRAplasmaIL29 5317407 DSt3R9-4A-UntrPMNs 5289423 DSt3R10-4B-PMNsIRAplasma 4222731 DSt3R11-4C-PMNsIRAplasmaTIC 6168213 DSt3R12-4D-PMNsIRAplasmaIL29 3913079 DSt3R13-5E-UntrPMNs 7334883 DSt3R14-5F-PMNspolyP 5474776 DSt3R15-5G-PMNspolyPTIC 5302910 DSt3R16-5H-PMNspolyPIL29 4700081 DSt3R17-5I-PMNsTIC 7456001 DSt3R18-5J-PMNsIL29 2988489 DSt3R19-6E-UntrPMNs 8807528 DSt3R20-6F-PMNspolyP 4759143 DSt3R21-6G-PMNspolyPTIC 7297544 DSt3R22-6H-PMNspolyPIL29 6365500 DSt3R23-6I-PMNsTIC 5918515 DSt3R24-6J-PMNsIL29 7014808 DSt3R29-8I-PMNsTIC 10978888 DSt3R30-8J-PMNsIL29 5593762 DSt3R25-8E-UntrPMNs 9796459 DSt3R26-8F-PMNspolyP 7037357 DSt3R27-8G-PMNspolyPTIC 7982874 DSt3R28-8H-PMNspolyPIL29 11540663 At http://genomics-lab.fleming.gr/fleming/external/DrStakos/metaseqr_DrStakos_run409/index.html you will find the metaseqR [1] differential gene expression analysis using the contrasts UntrPMNs134_vs_PMNsIRAplasma UntrPMNs134_vs_PMNsIRAplasmaTIC PMNsIRAplasma_vs_PMNsIRAplasmaTIC UntrPMNs134_vs_PMNsIRAplasmaIL29 PMNsIRAplasma_vs_PMNsIRAplasmaIL29 UntrPMNs568_vs_PMNspolyP UntrPMNs568_vs_PMNspolyPTIC UntrPMNs568_vs_PMNsTIC PMNspolyP_vs_PMNspolyPTIC PMNspolyP_vs_PMNsTIC PMNspolyPTIC_vs_PMNsTIC UntrPMNs568_vs_PMNspolyPIL29 UntrPMNs568_vs_PMNsIL29 PMNspolyP_vs_PMNspolyPIL29 PMNspolyP_vs_PMNsIL29 PMNspolyPIL29_vs_PMNsIL29 (note the used naming convention: in A_vs_B, A is always the reference). In the "Results" section, there are links to download the diff. expr. results under "DEG table", "Download the whole result list". The condition UntrPMNs134 consists of the samples: DSt3R1-1A-UntrPMNs DSt3R5-3A-UntrPMNs DSt3R9-4A-UntrPMNs The condition UntrPMNs568 consists of the samples: DSt3R13-5E-UntrPMNs DSt3R19-6E-UntrPMNs DSt3R25-8E-UntrPMNs Note that over all contrasts, there are only 6 DE genes. From the MDS plot: it might be worth removing DSt3R5-3A-UntrPMNs With best regards, Martin Reczko [1] Moulos P and Hatzis P “Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns.” Nucl. Acids Res. (2014) doi: 10.1093/nar/gku1273 http://nar.oxfordjournals.org/content/early/2014/12/01/nar.gku1273.abstract. ## Skip to content Using Biomedical Sciences Research Center Al. Fleming Mail with screen readers 16 of 29,496 Final deliverables DrStakos run409 Inbox x Δημήτριος Στάκος Jan 24, 2020, 2:58 PM (6 days ago) to me, alexmitsios, Pantelis, harokopos, papanikolaou, dstakos Dear all καθώς πληροφορούμαι από τον υπεύθυνο διαχείρισης των έργων ότι προχωρούν οι διαδικασίες για την έκδοση του τελικού τιμολογίου, παρακαλώ για τις δικές σας ενέργειες για την αποστολή των τελικών παραδοτέων της ανάλυσης. Για διευκόλυνση σας κοινοποιώ παρακάτω τις τελευταίες συνομιλίες Δημήτρης Στάκος Quoting Martin Reczko : > Dear Dr Mitsios, > > please excuse the delay, but now I understood that your samples have > biological pairs in the different conditions. > This type of analysis in not supported by the standard metaseqR tool we > employ, but I can perform a manual > paired analysis (using Deseq or EdgeR). > > BR, > Martin Reczko > > > > On Tue, Dec 11, 2018 at 11:12 AM Alexandros Mitsios > wrote: > >> Can a wilcoxon like test be performed? (4 different pairs before and after >> treatment) >> >> On Mon, Dec 10, 2018, 15:09 Martin Reczko > >>> >>> Dear Alexandros Mitsios, >>> >>> thank you for your message. >>> Before proceeding, I'd like to verify that these pairings do not have any >>> replicates and >>> thus, no p-values can be provided for the comparisons. The used Deseq >>> method will produce >>> p-values in this case, but these are of very limited scientific use. In >>> case you would >>> like to compare expression values without any assessment of their >>> significance, let me know. >>> >>> Best regards, >>> Martin Reczko >>> >>> >>> >>> On Mon, Dec 10, 2018 at 1:43 PM Alexandros Mitsios >>> wrote: >>> >>>> Excuse me for the + symbol it should be vs >>>> >>>> [1A(Untreated PMNs) vs 1B(PMNs+IRA plasma)] PAIR >>>> [3A(Untreated PMNs) vs 3B(PMNs+IRA plasma)] PAIR >>>> [4A(Untreated PMNs) vs 4B(PMNs+IRA plasma)] PAIR >>>> >>>> [5E(Untreated PMNs) vs 5F(PMNs+polyP)] PAIR >>>> [6E(Untreated PMNs) vs 6F(PMNs+polyP)] PAIR >>>> [8E(Untreated PMNs) vs 8F(PMNs+polyP)] PAIR >>>> >>>> On Mon, Dec 10, 2018, 13:22 Alexandros Mitsios >>> wrote: >>>> >>>>> Dear Dr. Reczko >>>>> >>>>> Each number describes cells (PMNs) derived from a single healthy >>>>> individual. The letters describe stimulations/inhibitions on these cells. >>>>> >>>>> In order to take a rough picture of the results we would firstly like a >>>>> paired analysis between these samples: >>>>> >>>>> [1A(Untreated PMNs)+1B(PMNs+IRA plasma)] PAIR >>>>> [3A(Untreated PMNs)+3B(PMNs+IRA plasma)] PAIR >>>>> [4A(Untreated PMNs)+4B(PMNs+IRA plasma)] PAIR >>>>> >>>>> [5E(Untreated PMNs)+5F(PMNs+polyP)] PAIR >>>>> [6E(Untreated PMNs)+6F(PMNs+polyP)] PAIR >>>>> [8E(Untreated PMNs)+8F(PMNs+polyP)] PAIR >>>>> >>>>> If the results of this analysis make sense we will proceed to further >>>>> analysis. >>>>> >>>>> Thank you in advance. Feel free to contact me if you have any further >>>>> questions. >>>>> >>>>> On Mon, Dec 10, 2018 at 12:47 PM Martin Reczko >>>>> wrote: >>>>> >>>>>> >>>>>> Dear Dr Stakos, >>>>>> >>>>>> in order to conduct the correct comparisions, >>>>>> can you please specify the additional contrast explicitly by >>>>>> giving the sample IDs for the contrasting groups? >>>>>> >>>>>> Best regards >>>>>> Martin Reczko >>>>>> >>>>>> -- >>>>>> Dr. Martin Reczko >>>>>> Bioinformatics Head >>>>>> Functional Genomics Laboratory and Genomics Facility >>>>>> Biomedical Sciences Research Center "Alexander Fleming" >>>>>> Technical Coordinator - ELIXIR Greece >>>>>> P.O. Box 74145 >>>>>> 16602, Varkiza, Greece >>>>>> Tel. +30-210-9656310 (ext. 144) >>>>>> FAX: +30-210-9653934 >>>>>> email: reczko@fleming.gr >>>>>> >>>>>> ---------- Forwarded message --------- >>>>>> From: Δημήτριος Στάκος >>>>>> Date: Fri, 7 Dec 2018 at 18:32 >>>>>> Subject: Re: DrStakos run409 >>>>>> To: Pantelis Hatzis >>>>>> Cc: >>>>>> >>>>>> >>>>>> Καλησπέρα >>>>>> >>>>>> Ευχαριστούμε την ομάδα σας για τη βοήθεια. >>>>>> Έχουμε ανοίξει τα αρχεία. Όλα πήγαν καλά και έχουμε κάποια πρώτη >>>>>> εικόνα. Θα παρακαλούσαμε να γίνει και μία σύγκριση "paired" στα >>>>>> δείγματα σύμφωνα με το επισυναπτόμενο αρχείο για να δούμε καλύτερα >>>>>> κάποιες μεταβολές. Δηλαδή σύγκριση μεταξύ δειγμάτων του ίδιου ατόμου >>>>>> πριν και μετά τις διεγέρσεις και αναστολές. >>>>>> >>>>>> >>>>>> >>>>>> Δημήτρης Στάκος >>>>>> τηλ. 6944996194 >>>>>> Assoc. professor of Cardiology >>>>>> Democritus University of Thrace >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Quoting Pantelis Hatzis : >>>>>> >>>>>> > Καλησπέρα, >>>>>> > >>>>>> > Ελπίζω ότι δεν έχετε προβλήματα με το link και τα υπόλοιπα data. Αν >>>>>> έχετε, >>>>>> > ειδοποιήστε μας. >>>>>> > >>>>>> > Χαιρετισμούς >>>>>> > >>>>>> > Παντελής >>>>>> > >>>>>> > Pantelis Hatzis, PhD >>>>>> > >>>>>> > Researcher Β, Division of Molecular Biology & Genetics >>>>>> > >>>>>> > Head of Fleming Genomics Facility >>>>>> > >>>>>> > Biomedical Sciences Research Center ‘Alexander Fleming’ >>>>>> > >>>>>> > 34 Fleming Street, 16672 Vari, Greece >>>>>> > >>>>>> > Tel: +30 210 9656310 ext. 175 >>>>>> > >>>>>> > Email: hatzis@fleming.gr >>>>>> > >>>>>> > >>>>>> > >>>>>> > On Mon, 3 Dec 2018 at 17:42, Pantelis Hatzis >>>>>> wrote: >>>>>> > >>>>>> >> Dear Dr Stakos, >>>>>> >> >>>>>> >> Please try the new link below, it should work this time, please >>>>>> note that >>>>>> >> it make take a few minutes to load completely, as the file is very >>>>>> large. >>>>>> >> Martin has attached a zip file with all figures for convenience as >>>>>> well. >>>>>> >> Please let us know if you have any problems. >>>>>> >> I am sorry for the inconvenience. >>>>>> >> >>>>>> >> Best regards >>>>>> >> >>>>>> >> Pantelis >>>>>> >> >>>>>> >> Pantelis Hatzis, PhD >>>>>> >> >>>>>> >> Researcher Β, Division of Molecular Biology & Genetics >>>>>> >> >>>>>> >> Head of Fleming Genomics Facility >>>>>> >> >>>>>> >> Biomedical Sciences Research Center ‘Alexander Fleming’ >>>>>> >> >>>>>> >> 34 Fleming Street, 16672 Vari, Greece >>>>>> >> >>>>>> >> Tel: +30 210 9656310 ext. 175 >>>>>> >> >>>>>> >> Email: hatzis@fleming.gr >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> ---------- Forwarded message --------- >>>>>> >> From: Martin Reczko >>>>>> >> Date: Mon, 3 Dec 2018 at 16:44 >>>>>> >> Subject: Re: DrStakos run409 >>>>>> >> To: Pantelis Hatzis >>>>>> >> Cc: Harokopos Vaggelis >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> http://genomics-lab.fleming.gr:8080/fleming/external/DrStakos/run409/metaseqr_DrStakos_run409/ >>>>>> >> >>>>>> >> For convenience, I also attach a zip file with all figures. >>>>>> >> >>>>>> >> BW, >>>>>> >> Martin >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >>> ---------- Forwarded message --------- >>>>>> >>> From: Pantelis Hatzis >>>>>> >>> Date: Fri, 30 Nov 2018 at 16:42 >>>>>> >>> Subject: Re: DrStakos run409 >>>>>> >>> To: >>>>>> >>> >>>>>> >>> >>>>>> >>> Καλησπέρα, >>>>>> >>> >>>>>> >>> Δυστυχώς όντως δε δουλεύει προσωρινά, κάτι χάλασε ξαφνικά, >>>>>> προσπαθούμε να >>>>>> >>> το λύσουμε, απλά μπορεί μάλλον θα το λάβετε αμέσως μετά το ΣΚ. >>>>>> Λυπάμαι πολύ >>>>>> >>> για την καθυστέρηση. >>>>>> >>> >>>>>> >>> Χαιρετισμούς >>>>>> >>> >>>>>> >>> Παντελής >>>>>> >>> >>>>>> >>> Pantelis Hatzis, PhD >>>>>> >>> >>>>>> >>> Researcher Β, Division of Molecular Biology & Genetics >>>>>> >>> >>>>>> >>> Head of Fleming Genomics Facility >>>>>> >>> >>>>>> >>> Biomedical Sciences Research Center ‘Alexander Fleming’ >>>>>> >>> >>>>>> >>> 34 Fleming Street, 16672 Vari, Greece >>>>>> >>> >>>>>> >>> Tel: +30 210 9656310 ext. 175 >>>>>> >>> >>>>>> >>> Email: hatzis@fleming.gr >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> On Thu, 29 Nov 2018 at 10:53, Alexandros Mitsios < >>>>>> alexmitsios@gmail.com> >>>>>> >>> wrote: >>>>>> >>> >>>>>> >>>> Καλημέρα, >>>>>> >>>> το link >>>>>> >>>> >>>>>> http://genomics-lab.fleming.gr/fleming/external/DrStakos/metaseqr_DrStakos_run409/index.html >>>>>> >>>> >>>>>> >>>> που περιέχει το metaseqR δεν λειτουργεί. >>>>>> >>>> >>>>>> >>>> ----- Προώθηση μηνύματος από Pantelis Hatzis >>>>>> ----- >>>>>> >>>> Ημερομηνία: Wed, 28 Nov 2018 17:51:27 +0200 >>>>>> >>>> Από: Pantelis Hatzis >>>>>> >>>> Θέμα: Fwd: DrStakos run409 >>>>>> >>>> Προς: Δημήτριος Στάκος >>>>>> >>>> >>>>>> >>>> Dear Dr Stakos, >>>>>> >>>> >>>>>> >>>> The analysis of your quant-seq experiment has finished. Please >>>>>> have a >>>>>> >>>> careful look at the information below. Feel free to get back to >>>>>> us with >>>>>> >>>> any >>>>>> >>>> questions or problems. >>>>>> >>>> >>>>>> >>>> Best regards >>>>>> >>>> >>>>>> >>>> Pantelis >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> Pantelis Hatzis, PhD >>>>>> >>>> >>>>>> >>>> Researcher Β, Division of Molecular Biology & Genetics >>>>>> >>>> >>>>>> >>>> Head of Fleming Genomics Facility >>>>>> >>>> >>>>>> >>>> Biomedical Sciences Research Center ‘Alexander Fleming’ >>>>>> >>>> >>>>>> >>>> 34 Fleming Street, 16672 Vari, Greece >>>>>> >>>> >>>>>> >>>> Tel: +30 210 9656310 ext. 175 >>>>>> >>>> >>>>>> >>>> Email: hatzis@fleming.gr >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> ---------- Forwarded message --------- >>>>>> >>>> From: Martin Reczko >>>>>> >>>> Date: Wed, 28 Nov 2018 at 17:41 >>>>>> >>>> Subject: DrStakos run409 >>>>>> >>>> To: Pantelis Hatzis >>>>>> >>>> Cc: Harokopos Vaggelis >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> Dear all, >>>>>> >>>> the analysis of your RNAseq experiment has finished. >>>>>> >>>> >>>>>> >>>> At >>>>>> >>>> >>>>>> >>>> >>>>>> http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=hg19&hubUrl=http://genomics-lab.fleming.gr/fleming/external/DrStakos/run409/hub.txt >>>>>> >>>> you will find tracks for all samples integrated for the UCSC >>>>>> genome >>>>>> >>>> browser. >>>>>> >>>> These tracks are sampled to smallest library >>>>>> (DSt3R7-3C-PMNsIRAplasmaTIC >>>>>> >>>> with 2853922 reads). >>>>>> >>>> >>>>>> >>>> sample n_reads >>>>>> >>>> --------------------------------------- >>>>>> >>>> DSt3R1-1A-UntrPMNs 4773312 >>>>>> >>>> DSt3R2-1B-PMNsIRAplasma 12401089 >>>>>> >>>> DSt3R3-1C-PMNsIRAplasmaTIC 8711500 >>>>>> >>>> DSt3R4-1D-PMNsIRAplasmaIL29 6595993 >>>>>> >>>> DSt3R5-3A-UntrPMNs 3669797 >>>>>> >>>> DSt3R6-3B-PMNsIRAplasma 7317844 >>>>>> >>>> DSt3R7-3C-PMNsIRAplasmaTIC 2853922 >>>>>> >>>> DSt3R8-3D-PMNsIRAplasmaIL29 5317407 >>>>>> >>>> DSt3R9-4A-UntrPMNs 5289423 >>>>>> >>>> DSt3R10-4B-PMNsIRAplasma 4222731 >>>>>> >>>> DSt3R11-4C-PMNsIRAplasmaTIC 6168213 >>>>>> >>>> DSt3R12-4D-PMNsIRAplasmaIL29 3913079 >>>>>> >>>> DSt3R13-5E-UntrPMNs 7334883 >>>>>> >>>> DSt3R14-5F-PMNspolyP 5474776 >>>>>> >>>> DSt3R15-5G-PMNspolyPTIC 5302910 >>>>>> >>>> DSt3R16-5H-PMNspolyPIL29 4700081 >>>>>> >>>> DSt3R17-5I-PMNsTIC 7456001 >>>>>> >>>> DSt3R18-5J-PMNsIL29 2988489 >>>>>> >>>> DSt3R19-6E-UntrPMNs 8807528 >>>>>> >>>> DSt3R20-6F-PMNspolyP 4759143 >>>>>> >>>> DSt3R21-6G-PMNspolyPTIC 7297544 >>>>>> >>>> DSt3R22-6H-PMNspolyPIL29 6365500 >>>>>> >>>> DSt3R23-6I-PMNsTIC 5918515 >>>>>> >>>> DSt3R24-6J-PMNsIL29 7014808 >>>>>> >>>> DSt3R29-8I-PMNsTIC 10978888 >>>>>> >>>> DSt3R30-8J-PMNsIL29 5593762 >>>>>> >>>> DSt3R25-8E-UntrPMNs 9796459 >>>>>> >>>> DSt3R26-8F-PMNspolyP 7037357 >>>>>> >>>> DSt3R27-8G-PMNspolyPTIC 7982874 >>>>>> >>>> DSt3R28-8H-PMNspolyPIL29 11540663 >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> At >>>>>> >>>> >>>>>> >>>> >>>>>> http://genomics-lab.fleming.gr/fleming/external/DrStakos/metaseqr_DrStakos_run409/index.html >>>>>> >>>> you will find the metaseqR [1] differential gene expression >>>>>> analysis >>>>>> >>>> using >>>>>> >>>> the contrasts >>>>>> >>>> >>>>>> >>>> UntrPMNs134_vs_PMNsIRAplasma >>>>>> >>>> UntrPMNs134_vs_PMNsIRAplasmaTIC >>>>>> >>>> PMNsIRAplasma_vs_PMNsIRAplasmaTIC >>>>>> >>>> >>>>>> >>>> UntrPMNs134_vs_PMNsIRAplasmaIL29 >>>>>> >>>> PMNsIRAplasma_vs_PMNsIRAplasmaIL29 >>>>>> >>>> >>>>>> >>>> UntrPMNs568_vs_PMNspolyP >>>>>> >>>> UntrPMNs568_vs_PMNspolyPTIC >>>>>> >>>> UntrPMNs568_vs_PMNsTIC >>>>>> >>>> PMNspolyP_vs_PMNspolyPTIC >>>>>> >>>> PMNspolyP_vs_PMNsTIC >>>>>> >>>> PMNspolyPTIC_vs_PMNsTIC >>>>>> >>>> >>>>>> >>>> UntrPMNs568_vs_PMNspolyPIL29 >>>>>> >>>> UntrPMNs568_vs_PMNsIL29 >>>>>> >>>> PMNspolyP_vs_PMNspolyPIL29 >>>>>> >>>> PMNspolyP_vs_PMNsIL29 >>>>>> >>>> PMNspolyPIL29_vs_PMNsIL29 >>>>>> >>>> >>>>>> >>>> (note the used naming convention: in A_vs_B, A is always the >>>>>> reference). >>>>>> >>>> In the "Results" section, there are links to download the diff. >>>>>> expr. >>>>>> >>>> results >>>>>> >>>> under "DEG table", "Download the whole result list". >>>>>> >>>> >>>>>> >>>> The condition UntrPMNs134 consists of the samples: >>>>>> >>>> DSt3R1-1A-UntrPMNs >>>>>> >>>> DSt3R5-3A-UntrPMNs >>>>>> >>>> DSt3R9-4A-UntrPMNs >>>>>> >>>> >>>>>> >>>> The condition UntrPMNs568 consists of the samples: >>>>>> >>>> DSt3R13-5E-UntrPMNs >>>>>> >>>> DSt3R19-6E-UntrPMNs >>>>>> >>>> DSt3R25-8E-UntrPMNs >>>>>> >>>> >>>>>> >>>> Note that over all contrasts, there are only 6 DE genes. >>>>>> >>>> From the MDS plot: it might be worth removing DSt3R5-3A-UntrPMNs >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> With best regards, >>>>>> >>>> Martin Reczko >>>>>> >>>> >>>>>> >>>> [1] Moulos P and Hatzis P “Systematic integration of RNA-Seq >>>>>> statistical >>>>>> >>>> algorithms for accurate detection of differential gene expression >>>>>> >>>> patterns.” Nucl. Acids Res. (2014) >>>>>> >>>> doi: 10.1093/nar/gku1273 >>>>>> >>>> >>>>>> >>>> >>>>>> http://nar.oxfordjournals.org/content/early/2014/12/01/nar.gku1273.abstract >>>>>> >>>> . >>>>>> >>>> >>>>>> >>>> ----- Τέλος προωθημένου μηνύματος ----- >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> ---------- Forwarded message ---------- >>>>>> >>>> From: Pantelis Hatzis >>>>>> >>>> To: "Δημήτριος Στάκος" >>>>>> >>>> Cc: >>>>>> >>>> Bcc: >>>>>> >>>> Date: Wed, 28 Nov 2018 17:51:27 +0200 >>>>>> >>>> Subject: Fwd: DrStakos run409 >>>>>> >>>> Dear Dr Stakos, >>>>>> >>>> >>>>>> >>>> The analysis of your quant-seq experiment has finished. Please >>>>>> have a >>>>>> >>>> careful look at the information below. Feel free to get back to >>>>>> >>>> us with any >>>>>> >>>> questions or problems. >>>>>> >>>> >>>>>> >>>> Best regards >>>>>> >>>> >>>>>> >>>> Pantelis >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> Pantelis Hatzis, PhD >>>>>> >>>> >>>>>> >>>> Researcher Β, Division of Molecular Biology & Genetics >>>>>> >>>> >>>>>> >>>> Head of Fleming Genomics Facility >>>>>> >>>> >>>>>> >>>> Biomedical Sciences Research Center ‘Alexander Fleming’ >>>>>> >>>> >>>>>> >>>> 34 Fleming Street, 16672 Vari, Greece >>>>>> >>>> >>>>>> >>>> Tel: +30 210 9656310 ext. 175 >>>>>> >>>> >>>>>> >>>> Email: hatzis@fleming.gr >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> ---------- Forwarded message --------- >>>>>> >>>> From: Martin Reczko >>>>>> >>>> Date: Wed, 28 Nov 2018 at 17:41 >>>>>> >>>> Subject: DrStakos run409 >>>>>> >>>> To: Pantelis Hatzis >>>>>> >>>> Cc: Harokopos Vaggelis >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> Dear all, >>>>>> >>>> the analysis of your RNAseq experiment has finished. >>>>>> >>>> >>>>>> >>>> At >>>>>> >>>> >>>>>> >>>> >>>>>> http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=hg19&hubUrl=http://genomics-lab.fleming.gr/fleming/external/DrStakos/run409/hub.txt >>>>>> >>>> you will find tracks for all samples integrated for the UCSC >>>>>> genome >>>>>> >>>> browser. >>>>>> >>>> These tracks are sampled to smallest library >>>>>> (DSt3R7-3C-PMNsIRAplasmaTIC >>>>>> >>>> with 2853922 reads). >>>>>> >>>> >>>>>> >>>> sample n_reads >>>>>> >>>> --------------------------------------- >>>>>> >>>> DSt3R1-1A-UntrPMNs 4773312 >>>>>> >>>> DSt3R2-1B-PMNsIRAplasma 12401089 >>>>>> >>>> DSt3R3-1C-PMNsIRAplasmaTIC 8711500 >>>>>> >>>> DSt3R4-1D-PMNsIRAplasmaIL29 6595993 >>>>>> >>>> DSt3R5-3A-UntrPMNs 3669797 >>>>>> >>>> DSt3R6-3B-PMNsIRAplasma 7317844 >>>>>> >>>> DSt3R7-3C-PMNsIRAplasmaTIC 2853922 >>>>>> >>>> DSt3R8-3D-PMNsIRAplasmaIL29 5317407 >>>>>> >>>> DSt3R9-4A-UntrPMNs 5289423 >>>>>> >>>> DSt3R10-4B-PMNsIRAplasma 4222731 >>>>>> >>>> DSt3R11-4C-PMNsIRAplasmaTIC 6168213 >>>>>> >>>> DSt3R12-4D-PMNsIRAplasmaIL29 3913079 >>>>>> >>>> DSt3R13-5E-UntrPMNs 7334883 >>>>>> >>>> DSt3R14-5F-PMNspolyP 5474776 >>>>>> >>>> DSt3R15-5G-PMNspolyPTIC 5302910 >>>>>> >>>> DSt3R16-5H-PMNspolyPIL29 4700081 >>>>>> >>>> DSt3R17-5I-PMNsTIC 7456001 >>>>>> >>>> DSt3R18-5J-PMNsIL29 2988489 >>>>>> >>>> DSt3R19-6E-UntrPMNs 8807528 >>>>>> >>>> DSt3R20-6F-PMNspolyP 4759143 >>>>>> >>>> DSt3R21-6G-PMNspolyPTIC 7297544 >>>>>> >>>> DSt3R22-6H-PMNspolyPIL29 6365500 >>>>>> >>>> DSt3R23-6I-PMNsTIC 5918515 >>>>>> >>>> DSt3R24-6J-PMNsIL29 7014808 >>>>>> >>>> DSt3R29-8I-PMNsTIC 10978888 >>>>>> >>>> DSt3R30-8J-PMNsIL29 5593762 >>>>>> >>>> DSt3R25-8E-UntrPMNs 9796459 >>>>>> >>>> DSt3R26-8F-PMNspolyP 7037357 >>>>>> >>>> DSt3R27-8G-PMNspolyPTIC 7982874 >>>>>> >>>> DSt3R28-8H-PMNspolyPIL29 11540663 >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> At >>>>>> >>>> >>>>>> >>>> >>>>>> http://genomics-lab.fleming.gr/fleming/external/DrStakos/metaseqr_DrStakos_run409/index.html >>>>>> >>>> you will find the metaseqR [1] differential gene expression >>>>>> analysis >>>>>> >>>> using >>>>>> >>>> the contrasts >>>>>> >>>> >>>>>> >>>> UntrPMNs134_vs_PMNsIRAplasma >>>>>> >>>> UntrPMNs134_vs_PMNsIRAplasmaTIC >>>>>> >>>> PMNsIRAplasma_vs_PMNsIRAplasmaTIC >>>>>> >>>> >>>>>> >>>> UntrPMNs134_vs_PMNsIRAplasmaIL29 >>>>>> >>>> PMNsIRAplasma_vs_PMNsIRAplasmaIL29 >>>>>> >>>> >>>>>> >>>> UntrPMNs568_vs_PMNspolyP >>>>>> >>>> UntrPMNs568_vs_PMNspolyPTIC >>>>>> >>>> UntrPMNs568_vs_PMNsTIC >>>>>> >>>> PMNspolyP_vs_PMNspolyPTIC >>>>>> >>>> PMNspolyP_vs_PMNsTIC >>>>>> >>>> PMNspolyPTIC_vs_PMNsTIC >>>>>> >>>> >>>>>> >>>> UntrPMNs568_vs_PMNspolyPIL29 >>>>>> >>>> UntrPMNs568_vs_PMNsIL29 >>>>>> >>>> PMNspolyP_vs_PMNspolyPIL29 >>>>>> >>>> PMNspolyP_vs_PMNsIL29 >>>>>> >>>> PMNspolyPIL29_vs_PMNsIL29 >>>>>> >>>> >>>>>> >>>> (note the used naming convention: in A_vs_B, A is always the >>>>>> reference). >>>>>> >>>> In the "Results" section, there are links to download the diff. >>>>>> expr. >>>>>> >>>> results >>>>>> >>>> under "DEG table", "Download the whole result list". >>>>>> >>>> >>>>>> >>>> The condition UntrPMNs134 consists of the samples: >>>>>> >>>> DSt3R1-1A-UntrPMNs >>>>>> >>>> DSt3R5-3A-UntrPMNs >>>>>> >>>> DSt3R9-4A-UntrPMNs >>>>>> >>>> >>>>>> >>>> The condition UntrPMNs568 consists of the samples: >>>>>> >>>> DSt3R13-5E-UntrPMNs >>>>>> >>>> DSt3R19-6E-UntrPMNs >>>>>> >>>> DSt3R25-8E-UntrPMNs >>>>>> >>>> >>>>>> >>>> Note that over all contrasts, there are only 6 DE genes. >>>>>> >>>> From the MDS plot: it might be worth removing DSt3R5-3A-UntrPMNs >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> With best regards, >>>>>> >>>> Martin Reczko >>>>>> >>>> >>>>>> >>>> [1] Moulos P and Hatzis P “Systematic integration of RNA-Seq >>>>>> statistical >>>>>> >>>> algorithms for accurate detection of differential gene expression >>>>>> >>>> patterns.” Nucl. Acids Res. (2014) >>>>>> >>>> doi: 10.1093/nar/gku1273 >>>>>> >>>> >>>>>> >>>> >>>>>> http://nar.oxfordjournals.org/content/early/2014/12/01/nar.gku1273.abstract >>>>>> >>>> . >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> -- >>>>>> >>>> Alexandros Mitsios, MSc >>>>>> >>>> Molecular Biologist & Geneticist >>>>>> >>>> Tel.: +306983645619 >>>>>> >>>> Email: alexmitsios@gmail.com >>>>>> >>>> Inflammation Research Group, Laboratory of Molecular Hematology, >>>>>> Dragana >>>>>> >>>> Campus, University Hospital of Alexandroupolis, 68100 >>>>>> Alexandroupolis, >>>>>> >>>> Greece. >>>>>> >>>> >>>>>> >>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Alexandros Mitsios, MSc >>>>> Molecular Biologist & Geneticist >>>>> Tel.: +306983645619 >>>>> Email: alexmitsios@gmail.com >>>>> Inflammation Research Group, Laboratory of Molecular Hematology, >>>>> Dragana Campus, University Hospital of Alexandroupolis, 68100 >>>>> Alexandroupolis, Greece. >>>>> >>>> Papanikolaou Nikos Jan 27, 2020, 12:39 PM (3 days ago) Καλημέρα και καλή εβδομάδα, είναι πραγματικά ευχάριστο το γεγονός ότι βρέθηκε λύση μετά το μεγάλο χρονικό διάστημα που μεσολάβησε απο την υποχρέωση εξόφλησης τη Martin Reczko Jan 27, 2020, 1:04 PM (3 days ago) Dear Pantelis, as indicated in my email from Dec 2018, the paired analysis asked for by D. Stakos is not part of our usual service. The paired analysis might pr Pantelis Hatzis 3:11 PM (5 hours ago) Hi Martin, I understand your point about the extra work and that this should have been addressed at the source. However, you should have clearly communicated fi Martin Reczko 4:59 PM (3 hours ago) to Pantelis Dear Pantelis, I admit having neglected their request and apologize for that. I'd like to emphasize however my exact wording in the email, stating that this is not supported by the standard tool we use and that I can perform the extra analysis, meaning that I have the means for it. These type of requests are difficult, as this is a novel analysis and I have to deal with this matter at least 2 full days exclusively. Please consider this in your assessment of this. BW Martin