[BioC] edgeR: effect of 'outlier' tags on differential expression calls

[alessandro.guffanti at genomnia.com]

Thanks for the useful suggestion, I will chase this up ! I have to say 
that MDS plot are not too useful in these cases, because there is not a 
general strong deregulation in one specific sample, but one localized to 
few genes and possibily in more than one sample. These 'tag bursts' are 
not infrequent in miRNA cancer analyses and they seem to be 'private' to 
some samples.

Yes, the output of the DEG calls ans sessionInfo() were originated from 
two different sessions, I forgot there was an update in the middle, 
thanks for pointing this.

Regards

Alessandro


On 4/25/2012 11:09 AM, Gordon K Smyth wrote:
> Dear Alessandro,
>
> You seem to giving examples of miRs that are expressed at a high 
> degree is just one sample.  The easiest way to deal with such miRs, if 
> you really don't want to detect them, is to filter out miRs that fail 
> to be expressed to a reasonable degree in at least four samples (since 
> your groups are of size four).  See for example pages 24-25 of the 
> edgeR user's guide, where this is done for the Dclk1 mouse case 
> study.  We often suggest cpm>1 for at least m samples, where m is the 
> minimum group size.
>
> Another obvious thing to do is to examine an MDS plot to identify 
> outlier samples.
>
> I also have to point out that the output in your email cannot be 
> correct, at least the output cannot all be from the same R session.  
> The sessionInfo() output says edgeR 2.6.0, but the column headings 
> show that the results being present are actually from an earlier 
> version of edgeR.
>
> I'd much rather see continuous code and output from one session, 
> rather than output snippets, without quite knowing how they were 
> obtained.
>
> Best wishes
> Gordon
>


-- 

Alessandro Guffanti - Head, Bioinformatics, Genomnia srl
  Via Nerviano, 31 - 20020 Lainate, Milano, Italy
     Ph: +39-0293305.702 Fax: +39-0293305.777
             http://www.genomnia.com
"When you're curious, you find lots of interesting things to do."
(Walt Disney)


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