Hi,
I am a newbie to bioinformatics and am trying to analyse RNASeq data with DeSeq.The dispersion plot for my data looks different from the the typical plots.I have attached two sample plots-the issue is that there is a sharp upper boundary and don't know how to interpret this!
I have tried the various options for sharingmode and fitytpe for my data and sometimes, default works but with a different sample list, I have to try a local fit or different sharing mode). I have four different conditions and there are 6-16 biological replicates for each, so sample size is not a problem.
Also, when I try to change estimate size factor command using the following, it does not work:
cds = estimateSizeFactors(cds,locfunc=shorth)
Am I doing anything wrong here?
Thanks for your help
I am a newbie to bioinformatics and am trying to analyse RNASeq data with DeSeq.The dispersion plot for my data looks different from the the typical plots.I have attached two sample plots-the issue is that there is a sharp upper boundary and don't know how to interpret this!
I have tried the various options for sharingmode and fitytpe for my data and sometimes, default works but with a different sample list, I have to try a local fit or different sharing mode). I have four different conditions and there are 6-16 biological replicates for each, so sample size is not a problem.
Also, when I try to change estimate size factor command using the following, it does not work:
cds = estimateSizeFactors(cds,locfunc=shorth)
Am I doing anything wrong here?
Thanks for your help
Comment