TDM file format.

Skip to first unread message

Luca Zammataro

Sep 23, 2014, 8:56:45 AM9/23/14
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)
and CNA..

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?



Michael P Schroeder

Sep 23, 2014, 6:10:29 PM9/23/14
Hi Luca

I am not quite sure about which files you are talking. Are you referring to a specific heatmap from Gitools datasets ( The TCGA data provenance is referenced from within the heatmap. If you are talking about example files that has been generated from tutorials, I would not recommend to use it for research as it may be incomplete.

The TDM format itself is a general format and the values each column contain depend on the original data.


You received this message because you are subscribed to the Google Groups "Gitools users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
Visit this group at

Luca Zammataro

Sep 24, 2014, 5:27:30 AM9/24/14
Many thanks Michael
the TDM files that i cited is present in the gitools sample data directories. Surely that file should be considered only a tutorial exercise.
Reply all
Reply to author
0 new messages