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Hi Gabriel,
I'm looking at a cancer transcriptomics dataset with Normal and Tumor samples, where I'm trying to quantify differences in pathways activity between Normal and Tumor tissue. I was able to run the analysis with the AESPCA_pVals() function and I'm now looking at the PC1 values for the EGFR pathway( which I undertand are a proxy for the activity of this pathway) (see picture below):
I expect/know that for the specific cancer type I'm studying the EGFR pathway is more active in Tumor than in Normal Tissue.
So my question is: How do I go from interpreting positive or negative PC1 values to to saying the X pathway is more active in a given condition ?
Thanks in advance for the help.
Best ,
-Mathias
The text was updated successfully, but these errors were encountered:
masaver
changed the title
Interpretation of PC1 values amon groups
Interpretation of PC1 values among groups
Oct 29, 2020
Hi Mathias,
I hate to be the bearer of bad news, but principal components are "unique up to a sign". That means that they can't be used to interpret whether or not a pathway is up-regulated or down-regulated, only that it is differentially regulated. We recommend that users target pathways for post-hoc analysis based on the p-values (or FDRs) yielded by the AESPCA_pVals() or SuperPCA_pVals() functions. In your case, it's mathematically appropriate to multiply the EGFR pathway PC by -1 and re-apply your statistical tests.
Hi Gabriel,
I'm looking at a cancer transcriptomics dataset with Normal and Tumor samples, where I'm trying to quantify differences in pathways activity between Normal and Tumor tissue. I was able to run the analysis with the AESPCA_pVals() function and I'm now looking at the PC1 values for the EGFR pathway( which I undertand are a proxy for the activity of this pathway) (see picture below):
I expect/know that for the specific cancer type I'm studying the EGFR pathway is more active in Tumor than in Normal Tissue.
So my question is: How do I go from interpreting positive or negative PC1 values to to saying the X pathway is more active in a given condition ?
Thanks in advance for the help.
Best ,
-Mathias
The text was updated successfully, but these errors were encountered: