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Old 05-25-2011, 01:53 AM   #1
johannes.helmuth
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Location: Berlin, Germany

Join Date: May 2011
Posts: 3
Default DESeq analysis without replicates for 16 tissues

Hello,

I am using DESeq to find differentially expressed genes in 16 tissues without any replicates.

Firstly I tried to set the conditions to 1x "X", 15x"N" and estimated the variance function with method="blind". This was not very sensitive and I could hardly identify any DE genes.

So I simply used the median of the 15 remainder tissues and could identify more. I know that this maybe is not the best way but it gave me better insight for further analyses.

Now I want to take a look at the variance estimation and its fit but all baseVar's in the variance fit are NA. Why is that? Maybe I did not understand the concept of baseMean and baseVar properly by reading the vignette and looking at the paper. Any help would be much appreciated...

Thanks in advance,
Johannes.
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