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> *P* *Per cortesia, prima di stampare questa e-mail pensate all'ambiente.* * Please consider the environment before printing this mail note.* ----------------------------------------------------------- Il Contenuto del presente messaggio potrebbe contenere informazioni confidenziali a favore dei soli destinatari del messaggio stesso. Qualora riceviate per errore questo messaggio siete pregati di cancellarlo dalla memoria del computer e di contattare i numeri sopra indicati. Ogni utilizzo o ritrasmissione dei contenuti del messaggio da parte di soggetti diversi dai destinatari è da considerarsi vietato ed abusivo. The information transmitted is intended only for the per...{{dropped:10}}