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gerstung-lab / MDS-expression

R code for Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes
http://dx.doi.org/10.1038/ncomms6901
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Its not an issue rather a request #1

Open kcmtest opened 2 years ago

kcmtest commented 2 years ago

This is fantastic paper a lot of things for me to learn just by looking at the analysis. I was trying to replicate the TCGA analysis

This part I tried to run but i don't see any output I would be really glad if you could let me know what is the other way of doing?

mycgds <-  CGDS("http://www.cbioportal.org/public-portal/")
tcgaAML <- getCancerStudies(mycgds)[1,1]
cases <- getCaseLists(mycgds,tcgaAML)[8,1]
g <-  lapply(split(as.numeric(entrez), seq_along(entrez)%/%500), function(genes) getProfileData(mycgds,genes,getGeneticProfiles(mycgds,tcgaAML)[2,1],cases)) ## load in batches of 500
g <- do.call("cbind", g)
mg14 commented 2 years ago

Thanks -- perhaps the query protocol for cBio has changed in the mean time? The paper was done in 2014. What are the return values for each command?

kcmtest commented 2 years ago

Thank you for the quick response Dr Moritz

the output i get

The error update it

mycgds <-  CGDS("http://www.cbioportal.org/public-portal/")
[1] "CGDS: 0x55bcf82ce978"
tcgaAML <- getCancerStudies(mycgds)[1,1]
> tcgaAML
[1] "<html class=\"cbioportal-frontend\">"
cases <- getCaseLists(mycgds,tcgaAML)[8,1]
 cases
[1] "    <title>cBioPortal for Cancer Genomics</title>"
g <-  lapply(split(as.numeric(entrez), seq_along(entrez)%/%500), function(genes) getProfileData(mycgds,genes,getGeneticProfiles(mycgds,tcgaAML)[2,1],cases)) ## load in batches of 500
 Error in `[.data.frame`(df, , 2) : undefined columns selected