Der BioC edgeR developers and users:

I am using edgeR for ncRNA transcriptome data analysis - ie mapping RNA seq
results only versus a ncRNA transcript database (bowtie from Color Space 
reads)

There seems to be, unsurprisingly, an high variability on these samples, 
which
affects obviously the FDR

However, what surprised us is that the CPM for the same samples in different
comparisons (TMM-normalized) are always very different

As an example:
*
**Comparison **A*

Transcript_ID 	logFC 	logCPM 	PValue 	FDR 	WT_4_CPM 	WT_7.CPM 	WT_10.CPM
ENST00000456355 	1.42 	10.91 	0.00001 	0.03283 	2843 	2926 	2631


*
**Comparison **B

*
Transcript_ID 	logFC 	logCPM 	PValue 	FDR 	WT_4_CPM 	WT_7.CPM 	WT_10.CPM


ENST00000456355 	0.91 	11.11 	0.00003 	0.00361 	190 	341 	157


Can TMM normalization affect so heavily the CPM values of the same 
samples in different comparisons,
or do we have something else wrong here ?

Thanks in advance for any feedback on this,

Alessandro G

---

R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods base

other attached packages:
[1] edgeR_3.4.0  limma_3.18.3


-- 
Alessandro Guffanti

Alessandro Guffanti

Head, Bioinformatics

*Genomnia srl*

Via Nerviano, 31/B -- 20020 Lainate (MI)

Tel. +39-0293305.702 / Fax +39-0293305.777

www.genomnia.com <http://www.genomnia.com>

alessandro.guffanti@genomnia.com <mailto:alessandro.guffanti@genomnia.com>

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