Question: PCA of Cuffdiff output
gravatar for Light
24 months ago by
Light20 wrote:

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.

rna-seq pca cuffdiff • 824 views
ADD COMMENTlink modified 24 months ago by igor7.3k • written 24 months ago by Light20

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.

ADD REPLYlink written 24 months ago by WouterDeCoster37k
gravatar for igor
24 months ago by
United States
igor7.3k wrote:

There is a visualization package cummeRbund specifically designed for working with Cufflinks/Cuffdiff output:

ADD COMMENTlink written 24 months ago by igor7.3k
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