PCA of Cuffdiff output

Question

[Light]

Hello, I have done bowtie workflow of virus infected human sample with control one with 6 samples and got 3k significant genes and would like to do PCA to check batch effect. can give a tutorial for PCA and batch effect removal ? Guide me right path.

[WouterDeCoster]

I doubt if doing PCA on 6 samples will give you enough information to reliably identify batch effects.

Did you use bowtie for alignment? Because that's not an appropriate for human RNA-seq.

Answer 1

[igor]

There is a visualization package cummeRbund specifically designed for working with Cufflinks/Cuffdiff output: http://compbio.mit.edu/cummeRbund/manual_2_0.html