[BioC] does contamination bother the normalization in transcriptome analysis

Maciej Jończyk mjonczyk at biol.uw.edu.pl
Sat Jun 1 09:29:01 CEST 2013

Dear Peter,

> 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, 
> e.g.
> 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).

Best Wishes,

Dr Maciej Jonczyk,
Department of Plant Molecular Ecophysiology
Faculty of Biology, University of Warsaw
02-096 Warsaw, Miecznikowa 1

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