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Question: Is there any prerequisites for taking correlation in genomic data?
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gravatar for Arman Shahrisa
4 months ago by
Arman Shahrisa10 wrote:

I know this question might not be related to Bioconductor but I couldn't think of anywhere else. When I take correlation between two genes, should I exclude genes that their expression is not meaningful? Additionally, should I exclude samples that their z-score is under e.g. z-score = 2? Or should I include all samples in a correlation?

 

Best regards,

Arman

ADD COMMENTlink modified 3 months ago by chris86380 • written 4 months ago by Arman Shahrisa10
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gravatar for chris86
3 months ago by
chris86380
UCL, United Kingdom
chris86380 wrote:

When is expression not meaningful?

We typically filter genes based on an abundance threshold before doing analyses (e.g. a CPM cut off), is this what you mean?

Should you exclude samples based on z-score?

I wouldn't remove samples unless they are clear outliers based on a global gene expression profile (e.g. using a PCA).

ADD COMMENTlink modified 3 months ago • written 3 months ago by chris86380
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