Question: ADVOCATE R package
1
gravatar for David_emir
11 months ago by
David_emir370
India
David_emir370 wrote:

Hi All,

I am using ADVOCATE R package to determine virtual expression from bulk gene expression. I am currently using TCGA-PAAD data. I have checked ADVOCATE manual, I am unable to understand the output generated. My question is how to interpret the output in this case? Can we use ADVOCATE trained data for cancer other than Pancreas? Here are the output files.

Thanks a lot for the help.

Regards Dave

rna-seq R advocate • 409 views
ADD COMMENTlink modified 11 months ago by kristoffer.vittingseerup3.0k • written 11 months ago by David_emir370

Could you post a link to the R package?

ADD REPLYlink written 11 months ago by kristoffer.vittingseerup3.0k

It is here, Its Github repository.

ADD REPLYlink written 11 months ago by David_emir370
1
gravatar for kristoffer.vittingseerup
11 months ago by
European Union
kristoffer.vittingseerup3.0k wrote:

I would probably not apply ADVOCATE to other cancer types than Pancreas. ADVOCATE is (one of many) tools that require a set of "pure" expression profiles (reference profiles) from all cells you want to infer expression from in the bulk data. That also means results will be unreliable if your set of reference profiles is not adequate. In their paper they extract the reference dataset from Pancreas cancers - but it is very likely other cancer types will have another set of reference profiles (even the same cell types will have different profiles) thereby undermining the results. So unless you have a set of reference profiles for you data you should probably not use any such tools.

ADD COMMENTlink written 11 months ago by kristoffer.vittingseerup3.0k
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