Dear Panagiotis,

a quick question:
Why do samples that are not part
of any contrast affect the filtering?


http://genomics-lab.fleming.gr/fleming/GPlab/run183/metaseqr_CtrlSal_vs_CtrlArs
http://genomics-lab.fleming.gr/fleming/GPlab/run183/targets-run183.txt
vs
http://genomics-lab.fleming.gr/fleming/GPlab/run183/metaseqr_CtrlSal_vs_CtrlArs_only
http://genomics-lab.fleming.gr/fleming/GPlab/run183/targets-run183.txt2

BW,
Martin

Dear Marina,

pls. see the results at:
http://genomics-lab.fleming.gr/fleming/GPlab/run179/metaseqr_CtrlSal_vs_TgSal/index.htmle

Differential expression analysis for the contrasts CtrlSal versus
TgSal using the Bioconductor package edgeR

The final numbers of differentially
expressed genes were (per contrast): for the contrast CtrlSal versus
TgSal, 384 (2) statistically significant genes were found with a
p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 10
(2) were up-regulated, 2 (0) were down-regulated and 372 (0) were not
differentially expressed according to an absolute fold change cutoff
value of 1 in log2 scale.


And at:
http://genomics-lab.fleming.gr/fleming/GPlab/run183/metaseqr_CtrlArs_vs_TgArs/index.html

Differential expression analysis for the contrasts CtrlArs versus
TgArs using the Bioconductor package edgeR

The final numbers of differentially
expressed genes were (per contrast): for the contrast CtrlArs versus
TgArs, 322 (2) statistically significant genes were found with a
p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 28
(1) were up-regulated, 8 (1) were down-regulated and 286 (0) were not
differentially expressed according to an absolute fold change cutoff
value of 1 in log2 scale.

The other contrasts will follow,
we can discuss this all later.

Best wishes,
Martin