I have some questions concerning TDM files (Multi-value data matrix)?
In the Gitools documentation, users can find a description of TDM files:
"TDM file format is a tab delimited file that has contains multiple values per row (gene) and column (sample). The first line is a header line following a line for each cell."
The TDM header in general refers to:
Patient ID (column)
Gene Name (row)
DNAChip Expression value from Microarrays (expression)
1) What exaclty means 0, 1, 2? in the CNA column? (0 no alteration, 1, upregulation, 2 downlregulation?)
2) How the expression value is calculated in the "expression" column? Is it a LogCNA, or seq_v2_mrna, or 2*(2^x) value?
3) In the Gitools distribution there is a TDM file named "tcga-gbm.tp53.pathway.tdm.gz". I guess that this file come from GBM TCGA expression files. My question is: what study was taken in consideration in the TDM file? GBM_Cell_2013, or GBM_Nature_2008 or Glioblatoma Multiforma Provisional TCGA?
4) The tcga-gbm.tp53.pathway.tdm.gz header contains information that I assumed were previously calculated: expr cancer-vs-normal and expr median-centered. In what way these values were calculated? How I can find the "normal" expression values, to recalculate the expr cancer-vs-normal value?