Question: PCA of Cuffdiff output
0
gravatar for Light
2.4 years 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 • 960 views
ADD COMMENTlink modified 2.4 years ago by igor7.9k • written 2.4 years 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 2.4 years ago by WouterDeCoster40k
1
gravatar for igor
2.4 years ago by
igor7.9k
United States
igor7.9k 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 2.4 years ago by igor7.9k
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