[BioC] does contamination bother the normalization in transcriptome analysis
mjonczyk at biol.uw.edu.pl
Sat Jun 1 09:29:01 CEST 2013
> i got 70458 transcripts of one worm by de novo assembly,
> but i found 11825 of them are Escherichia contamination.
> i think if i donot remove them,it will bother the later analysis,
> normalization ??
As normalization relays mainly on intensities (except methods when you
select control probes)
you should leave E. coli data for normalization and remove it
These 1/7 non interesting for you probes would compromise further
differential expression analysis
(inflated fdr cutoff value).
Dr Maciej Jonczyk,
Department of Plant Molecular Ecophysiology
Faculty of Biology, University of Warsaw
02-096 Warsaw, Miecznikowa 1
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