RPGM is the ratio of mapped reads per gene model (either the gene length or the sum of exon lengths)
see https://bioconductor.org/packages/release/bioc/manuals/metaseqR/man/metaseqR.pdf
(page 96, section "export.scale"). This is related but not identical to RPKM values.
The read counts are normalized using the normalization algorithm in the DESq package.

With kind reagrds,
Martin



Dear Pantelis,

at
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/hub.txt
are tracks for all samples, normalized to the smallest library (SK3R16-Lbil22-7m) containing 2050808 reads.

The number of reads per sample are:
ID                n_reads
SK3R13-Lbctrl4    4449523
SK3R14-Lbctrl5    4225915
SK3R15-Lbctrl6    6214237
SK3R17-Lbil22-8   4315688
SK3R1-Tbctrl2     10362675
SK3R20-Lcctrl4    3178634
SK3R21-Lcctrl6    4492990
SK3R22-Lcil22-8   4194432
SK3R23-Lcil22-11  3218529
SK3R24-Lcil22-12  4056587
SK3R2-Tbctrl3     3972441
SK3R3-Tbctrl4     3843997
SK3R5-Tbil22-11   3009148
SK3R7-Tdctrl2     2892139
SK3R8-Tdctrl3     2889468
SK3R9-Tdctrl6     3127175

Preparing the tracks I've noted that the following samples had additional sequening:
ID                n_reads
SK3R4-Tbil22-7m   2338876
SK3R6-Tbil22-12m  2876788
SK3R10-Tdil22-9m  4051216
SK3R11-Tdil22-10m 2909714
SK3R12-Tdil22-11m 2979090
SK3R16-Lbil22-7m  2050808
SK3R18-Lbil22-9m  2055076
SK3R19-Lcctrl3m   2328278

The diff. exp. analysis for all pairings for these samples (execept TbctrlVSTdctrl that was not affected) was redone.
All cases show more DE genes (except Lcctrl_vs_Lcil2, 2 genes lost).


Pls see:
breast cancer clones:
Tb (no stim.) vs. Tb (IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/v2/metaseqr_quantseq_TbctrlVSTbil22/

Td (no stim.) vs. Td (IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/v2/metaseqr_quantseq_TdctrlVSTdil22/

Tb (no stim.) vs. Td (no stim)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/v2/metaseqr_quantseq_TbctrlVSTdctrl/

Tb (IL-22) vs. Td(IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/v2/metaseqr_quantseq_Tbil22VSTdil22/


lung cancer clones:
Lb (no stim.) vs. Lb (IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/v2/metaseqr_quantseq_LbctrlVSLbil22/

Lc (no stim.) vs. Lc (IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/v2/metaseqr_quantseq_LcctrlVSLcil22/

Lb (no stim.) vs. Lc (no stim)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/v2/metaseqr_quantseq_LbctrlVSLcctrl/

Lb (IL-22) vs. Lc (IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/v2/metaseqr_quantseq_Lbil22VSLcil22/



BW,
Martin





---------- Forwarded message ----------
From: Anamarija Markota <ana.markota@gmail.com>
Date: 30 November 2017 at 12:33
Subject: Re: Update
To: Pantelis Hatzis <hatzis@fleming.gr>, "Privatdozent Dr. med. Sebastian Kobold" <sebastian.kobold@med.uni-muenchen.de>
Cc: Javier Suárez Gosálvez <javi_suagosal@hotmail.com>


Dear Dr. Hatzis,

thank you very much for the update. We would like to do following comparisons:

breast cancer clones:
Tb (no stim.) vs. Tb (IL-22)
Td (no stim.) vs. Td (IL-22)
Tb (no stim.) vs. Td (no stim)
Tb (IL-22) vs. Td(IL-22)

lung cancer clones:
Lb (no stim.) vs. Lb (IL-22)
Lc (no stim.) vs. Lc (IL-22)
Lb (no stim.) vs. Lc (no stim)
Lb (IL-22) vs. Lc (IL-22)

Please let me know if you need any further information.

Kindest regards

Ana



breast cancer clones:
Tb (no stim.) vs. Tb (IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/metaseqr_quantseq_TbctrlVSTbil22/

Td (no stim.) vs. Td (IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/metaseqr_quantseq_TdctrlVSTdil22/

Tb (no stim.) vs. Td (no stim)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/metaseqr_quantseq_TbctrlVSTdctrl/

Tb (IL-22) vs. Td(IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/metaseqr_quantseq_Tbil22VSTdil22/





lung cancer clones:
Lb (no stim.) vs. Lb (IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/metaseqr_quantseq_LbctrlVSLbil22/

Lc (no stim.) vs. Lc (IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/metaseqr_quantseq_LcctrlVSLcil22/

Lb (no stim.) vs. Lc (no stim)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/metaseqr_quantseq_LbctrlVSLcctrl/

Lb (IL-22) vs. Lc (IL-22)
http://genomics-lab.fleming.gr/fleming/external/SKobold/run374/metaseqr_quantseq_Lbil22VSLcil22/