Question: Correlation analysis between gene expression & tumor purity
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gravatar for newbio17
21 months ago by
newbio17240
newbio17240 wrote:

What I have seen previously in papers is that the authors find genes that are highly correlated with tumor purity.

I'm mainly confused in Paper #1, when author says:

"Spearman correlations were calculated between their expression and tumor purity to generate a ranked list of genes."

If you have a matrix consisting of 50 samples where they are separated into groups of 10 according to the tumor type (5 groups) and 20,000 rows for genes, how do you perform correlation analysis with 50 tumor purity values for the 50 samples to identify the genes that are highly correlated?

ADD COMMENTlink modified 21 months ago by Devon Ryan97k • written 21 months ago by newbio17240
2
gravatar for Devon Ryan
21 months ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

They just computed the correlation between each row of gene expression values (50 values) and the 50 purity values and then creating a ranked list of the results. In R you would do that with cor() and apply().

ADD COMMENTlink written 21 months ago by Devon Ryan97k

Thank you. Your posts are always helpful.

ADD REPLYlink written 21 months ago by newbio17240
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