Thank you !
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Differential expression method for N=1 (Treatment) vs multiple control samples
Can some one please suggest what is the best normalization and differential expression method for RNASEQ N=1 treatment vs N control samples (both treatment and control samples generated from different centers,libraries and sequencers)
Thanks in advance
Regards
nitin
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Ram
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prodduturin •
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1 answer
As Devon said, you can not expect reliable results, but if you do want to try, check GFold,
http://bioinformatics.oxfordjournals.org/content/28/21/2782.long
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If your treatment and control samples were generated by different centers then no method will produce reliable results unless you know a priori of a set of genes unaffected by the treatment.
Thank you !
Do you recommend gfold? for exploratory investigation of RNA-seq with no replicates? or are there others that will still run with no replicates? Thanks.