[BioC] DESeq Fold-Change calculation
schaffer at scripps.edu
Mon Aug 27 17:43:14 CEST 2012
Yes, I was incorrect in saying that the FC calculation used unnormalized values.
I have been given 2 equivalent datasets (8 controls and 8 treated) and need to
"Show 'concordant' or reproducible hits". Using DESeq, dataset B gave only
21 (set B) transcripts significant compared to 431 for dataset A. Turns out
That the stdev was higher for set B.
Dataset control treat
A 76 130
B 96 164
The package edgeR is giving more usable results for the 2 datasets :
416 (A) and 145 (B) transcripts with 76 overlapping. Perhaps the variance
Is controlled better in edgeR?
From: Simon Anders [mailto:anders at embl.de]
Sent: Monday, August 27, 2012 2:11 AM
To: Lana Schaffer; bioconductor at r-project.org
Subject: Re: [BioC] DESeq Fold-Change calculation
On 2012-08-26 13:16, Lana Schaffer wrote:
> I haven't checked to see if there has already been a discussion about
> the fold-change Calculation in DESeq, but I have found that the fold-change is calculated using the
> Raw count values and not the normalized count values. I usually use the fold-change
> With a cutoff value, but this isn't valid if the unnormalized counts are used for
> The FC calculation. Any thoughts about this?
Of course, fold change is calculated using the normalized counts -- unless you have uncovered a very strange bug. Could you demonstrate with an example what you mean?
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