I was wondering where the links are for the dataset mentioned in the CVE package in order to try the pipeline of the vignette. The dataset seems to be concatenated from the individual RNAseq2 level 3 files which is quite obscure to me. In the vignette the author stated the original dataset has been moved from TCGA data portal to Genomic Data Commons. I spent some time and found this link, but not sure this is correct, for example, one file is Table_S1D.xlsx instead of Table_S1D.txt, although it can be easily converted.

There are two compressed files as tar.gz for RNA expression with the second file 130k of size:

• Level 3 Data Archive [DCC]:unc.edu_SKCM.IlluminaHiSeq_RNASeqV2.Level_3 [tar.gz](3.2G)
• mage-tab Archive [DCC]: unc.edu_SKCM.IlluminaHiSeq_RNASeqV2.mage-tab [tar.gz]

Can anybody confirm this for me? Thanks a lot!

Yifang

The first file above is the one that you need for the data. The metadata (sample information) is in the second file.