[BioC] does contamination bother the normalization in transcriptome analysis

[Maciej Jończyk]

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 
afterwards.
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
Poland


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