Question About Tcga Snp-Array Data

Question

[liu4gre]

I am trying to use TCGA SNP data, the it is level-2. There are 4 types of data for each samples: genotype.dat, intensities.dat, alleleSpecificCN.dat, pairedcn.dat. Would you please tell me what each data contains? And how can I get the level-3 data (segmented.data and snp_analysis.seg.txt) from these level-2 data?

Thanks.

Answer 1

[David Quigley]

The TCGA has extensive documentation on the consortium website. In increasing order of specificity:

https://tcga-data.nci.nih.gov/tcga/tcgaDataType.jsp

https://wiki.nci.nih.gov/display/TCGA/TCGA+Data+Primer

https://wiki.nci.nih.gov/display/TCGA/SNP+array-based+data

[liu4gre]

Thanks. Do you know which software/package they use to process the data? I am sorry that I am new to this area and really not familiar with this database. Would you please tell me the content of pairedcn.dat? And is the level-3 data only for CN? not for SNP anymore? Thanks.

[David Quigley]

Sorry, I don't know all of the details. TCGA is a huge effort and sometimes they have processed the data in more than one way for a given level. I suggest you read the documentation as it should tell you what you need to know.