About TCGA CNV data processing

Question

[sumitguptabt]

Hello all, I am looking at the Level 3 CNV files on TCGA. I have a one questions:

I download copy number variance data from the TCGA database and mapped genomic regions to gene symbols using GenomicRanges and bioMart as suggested by Kevin Blighe in How to extract the list of genes from TCGA CNV data ) post. Now I want to convert the log output to liner output for making a real change in copy number. However, the output has a different sign. ("Log_Seg" column represents the log base 2 output while "Seg_value" is liner value of "Log_seg" column). Log to liner scale is also experimental requirement.

           GeneSymbol  Log_Seg   Seg_value
240        ARHGEF16    0.0026    -8.587273
467        MEGF6       0.0001    -13.287712
638        TPRG1L      0.0004    -11.287712
903        WRAP73     -0.0043       NaN
1007       TP73        0.0142    -6.137965

This change in sign changes the whole interpretation of amplification vs. deletion.

Please guide me that how do I process the data further?

Thanks for any help,

Answer 1

[Kevin Blighe]

Hi,

I think that it is the other way, i.e., Log_Seg is linear, and Seg_value is log2 ('log [base 2]'):

log2(0.0142)
[1] -6.137965

log2(0.0026)
[1] -8.587273

So, you should be able to proceed with my other postings via the Seg_value column.

kevin