Hello,
I have a very basic question because I have never worked with SNPS or CNVs:
If I have many tumor samples and many normal samples from different patients, am I supposed to be calling the CNVS and SNPS for each patient? Like: tumor patient 1 vs normal patient 1
Or am I supposed to compare all at the same time like in a differential expression analysis?
Thank you
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Pin.Bioinf
You should compare the pair samples (tumor and control) from the same patient. Not all tum vs all control.
Thank you! And then, what is the statistics applied to draw a conclusion from all individual comparisons? (Im not there yet, but its curiosity)
We don't know what your biological question is.
If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
As Wouter mentioned it depends on the related biological question.
Okay. What I actually want to observe is if there is a SNP and / or CNA change in a same tumor along time. So I am using tumor at time 1 as control and tumor at time 2 as tumor in Varscan . Is that correct? Because I want to see the changes in between. Or maybe i should call for snps and cnas individually for each tumor (like varscan allows to do) and then compare both .tsv files and see if there is a difference in there.?
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