> 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
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
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
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
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