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Old 01-13-2012, 04:27 AM   #1
Andrea Apolloni
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Location: Italy

Join Date: Jan 2012
Posts: 2
Default DESeq without biological replicates (dataset: Marioni et al.)

Hello,
I'm trying to use DESeq (version 1.6.1) for differential analysis of the dataset of Marioni et al.
This dataset contains the counts of 32000 genes sequenced from liver and kidney cells of only one patient. For each condition (liver and kidney), the authors sequenced the samples on different lanes of the machine. This results in replication techniques, but not biological replicates.

Following the directions of the vignette, I summed the counts of technical replicates of liver and kidney. So, now I have a sample for kidney and a sample for liver, for each gene.

I'm trying to use the estimateDispersions function with the parameters method="blind" and sharingMode="fit-only".
By doing so I get a warning: "In parametricDispersionFit(means, disps) : Dispersion fit did not converge."
If I try to use the estimateDispersions function with the parameters method="blind", sharingMode="fit-only" and also fitType="local", the warning disappears.

Is this a correct choice of parameters, with this dataset?

Thanks
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