Different normalization methods with count data

[greener]

Hello folks, Quick question. I have RNAseq count data sets which I would like to analyze together. Experimentall they are similair they only differ by their depths of coverage . One set has about 30 million reads and the other has about 70 million. When you look at these files in an MDS plot you can see they are clearly different. Can anyone recommend a good aggressive normalization technique? Something similar to combat? I have tried the built in ones in DEseq and EDGER but would like to use one that's slightly more aggressive. Any suggestions are appreciated .thanks
-Rich

[dpryan]

Is it just the size normalization that's not really working sufficiently for you or are there other batch effects that you need to address (you mentioned combat, so I wonder about that)? It'd be helpful if you provided some more details and preferably a plot or two to demonstrate what's functioning poorly. You'll likely receive a higher quality of feedback then

[Simon Anders]

An MDS plot on raw count data is very unlikely to give any useful information. You should not use it for this purpose.