Differential expression method for N=1 (Treatment) vs multiple control samples

Question

[prodduturin]

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

[Devon Ryan]

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.

[prodduturin]

Thank you !

[nathan bowen]

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.

Answer 1

[Tky]

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

[prodduturin]

Thank you !