Dear all,

I recently started using cBioPortal and struggling to understand the terminologies used and what is the importance and application of a particular one over another and apologies for a long and naive question.

The aim of my study is to understand the mutational profile.

for the cancer study "prad_su2c_2015", I got geneticprofile as following

prad_su2c_2015_gistic Putative copy-number alterations from GISTIC prad_su2c_2015_rna_seq_mrna mRNA expression / polyA (RNA Seq RPKM) prad_su2c_2015_rna_seq_mrna_median_Zscores mRNA Expression z-Scores (RNA Seq RPKM) prad_su2c_2015_log2CNA Log2 copy-number values prad_su2c_2015_mutations Mutations prad_su2c_2015_rna_seq_capture mRNA expression / capture (RNA Seq RPKM) prad_su2c_2015_rna_seq_mrna_capture_Zscores mRNA Expression / capture z-Scores (RNA Seq capture)

Now, here is where I am confused:

1. what is the difference between "mRNA expression / polyA" and "mRNA expression/capture"
2. Should I use the normal score or with z-Scores?
3. what is the difference between "Putative copy-number alterations from GISTIC" and "Log2 copy-number values" and "Relative linear copy-number values" ( Relative linear copy-number values is found in the genetic profile of "prad_tcga_pub")

I used command

mutationdata <- getMutationData(mycgds,"prad_su2c_2015_all","prad_su2c_2015_mutations",c(genes_list[1:nrow(genes_list),1]))

where c(genes_list[1:nrow(genes_list),1]) is the list of genes I am interested in.

The resulting file has function impact score but I am not able to understand what does the following characters means functional_impact_score M L NA N H

The mutation_extended results don't show Variant_Type (i.e. SNP, DNP, TNP, ONP, INS, DEL, or Consolidated)

Now when I ran the following command

mutationdata2 <- getMutationData(mycgds,"prad_su2c_2015_all","prad_su2c_2015_gistic",c(genes_list[1:nrow(genes_list),1]))

The resulting file was empty. So does it mean that there is no CNA predicted by GISTIC or I have run a wrong command?

thanks in advance