TCGA Data: Local Update by Pablo Freire
Pablo Freire, working with Dr. Jonas Almeida on the TCGA data, has posted new data to our (secure) TCGA intranet site. If you are part of our MDACC TCGA group and wish to have access to these data, please send an email to Oliver Bogler.
Pablo writes:
The data is presented as tab-delimited files and can be imported to excel. For the expression and copy number data, those values are calculated for every affymetrix probe position. Sequence data are the exact tab-delimited files from the TCGA portal.
For the expression and copy number files, I did the following:
Expression platform: Affymetrix U133A plate set, performed by Broad Inst.
Copy number platoform: Agilent 244A aCGH, performed by Harvard Medical School.
For expression, the raw data (CEL files) were retieved from the TCGA portal. For the copy number, the normalized data was used.
Expression data normalized with RMA.
Copy number data segmented with CBS.
For every affymetrix probe position, I eliminated genes that were not annotated at the RefSeq or probes that either don't match anywhere or match in more than one location in the genome.
Also, for every affymetrix probe position, I calculated the copy numeber associated by getting the mean values of the copy number probes within the span of the gene.
Just one sample per patient was used. In the cases where there were multiple samples per patient, the first one was used, yielding a total of 207 patients.
Links to the data are (access & password required):
