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,