I tried to download the CGGA expression data, but the server timed out. Based on the # of samples, I expect it might be much larger than the TCGA data files, and therefore is causing a server or gateway issue. I noticed a similar post in the community forum, GlioVis user group. I used 'Explore' tab, 'Tumor Type: All', 'Download complete dataset > Download expression data'), and got the error message "502 Bad Gateway The server returned an invalid or incomplete response." Is this a known issue that will not be fixed soon?
The TCGA pheno data 538 sample files have 3 subtypes, no neural. Did you recalculate the subtypes or did you download from the source this way?
I just noticed that regardless of the pheno dataset related to TCGA I intended to download from your site, I always get one set of 538 samples in a 72kb text file, even though according to your home page HG-UG133A has 528 samples, Agilent-4502A has 489 samples, and RNA-Seq has 156 samples. I got to the download button two different ways with the same results: 1) Explore>Summary>Dataset download, or 2) Explore>Survival>Dataset download. The expression files are all vastly different sizes, so I expect them to be accurate. Am I downloading the pheno files improperly, or is this a glitch in the system?