Question: PCA of Cuffdiff output
gravatar for Light
19 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 • 694 views
ADD COMMENTlink modified 19 months ago by igor6.8k • written 19 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 19 months ago by WouterDeCoster32k
gravatar for igor
19 months ago by
United States
igor6.8k wrote:

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

ADD COMMENTlink written 19 months ago by igor6.8k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1689 users visited in the last hour