Hi all,

I was checking DESeq normalization success for my samples following the suggestions in this post : https://stat.ethz.ch/pipermail/bioconductor/2010-October/035933.html. I observed that filtering down to the genes that are present in both case and control samples improved normalization  (visualized by plotting as per the post), but for a few samples ,say  3 samples these procedures did not help, and I tried calculating shorth estimator (again as per the post) and this did n't help either. My question is what should I follow for the normalization of these samples ?



Regards,
Sudeep.

	[[alternative HTML version deleted]]