Question: PCA of Cuffdiff output
0
gravatar for Light
22 months ago by
Light20
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 • 765 views
ADD COMMENTlink modified 22 months ago by igor7.1k • written 22 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 22 months ago by WouterDeCoster35k
1
gravatar for igor
22 months ago by
igor7.1k
United States
igor7.1k wrote:

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

ADD COMMENTlink written 22 months ago by igor7.1k
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