TDM file format.

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Luca Zammataro

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Sep 23, 2014, 8:56:45 AM9/23/14
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Hi,
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?

Thanks!

Luca

Michael P Schroeder

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

I am not quite sure about which files you are talking. Are you referring to a specific heatmap from Gitools datasets (www.gitools.org/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.

Best,
Michael

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Luca Zammataro

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Sep 24, 2014, 5:27:30 AM9/24/14
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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.
Best,
Luca
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