Re: [galaxy-user] Identification of replicate outlier

> c) if you can create an appropriate input matrix (read counts by exon > or other contig for each sample eg), the Principal Component Analysis > tool might be helpful (library size normalization is one devil that > lies in the detail and it's not quite the same as MDS - see below) I like startin

Re: [galaxy-user] Identification of replicate outlier

Hi Ross, Thanks for the suggestions. I'm aware that this is not really a Galaxy-specific question, and I've been browsing through SeqAnswers and found a couple of suggestions using edgeR or DESeq, but nothing for Tuxedo suite. However, I have no experience with either of these tools, so I was wond

Re: [galaxy-user] Identification of replicate outlier

Hi Dave, This is an interesting and non-trivial question that extends well beyond Galaxy - and there's no simple solution AFAIK Defining an 'outlier' tends to boil down to subjective judgement in most real cases I've seen. EG: see http://comments.gmane.org/gmane.science.biology.informatics.conduct

[galaxy-user] Identification of replicate outlier

Hello list, I've been analyzing an experiment with two groups each with three replicates. My workflow was TopHat (paired end) -> Cufflinks -> CuffDiff. Unfortunately, there are not many significant differences identified by CuffDiff. I am wondering whether one of my replicates might be an outlier