Hi Simon, Thank you for your interest, I was able to trace back the 'normalization problem' to some bad quality reads that were not trimmed off from the fastq file, and by the way your suggestion to use MA plot instead of normalization was very helpful, gave me a much clear idea on the read count mappings. Regards, Sudeep. ________________________________ From: Simon Anders To: bioconductor@r-project.org Sent: Wednesday, 8 August 2012 12:08 PM Subject: Re: [BioC] DESeq normalization Hi Sudeep On 2012-08-08 08:28, sudeep s wrote: > As you said in the post, I was plotting to see if the size factor was > hitting the median, in some samples (3), the size factor was way off > the median and hence I tried shorth, but this didn't help either, and > I tried filtering down the genes (filtering genes on row sums for > 10,15,20, 25...) but again in the plot size factor was way off, so I > was wondering what I should follow. I guess you'd need to post your plots to the list. It's hard to advise without seeing them.   Simon _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]