Which is the best way for GSVA on TCGA dataset
Dear Communities,
My question is which kind of data from TCGA is the best way for GSVA analysis. This post (GSVA R packages) demonstrated the best way is based on row counts data. However, FPKM, TPM, RPKM are also acceptable for GSVA (kcdf = 'Gaussian'). So I wonder why row count is the best way for GSVA. Any suggestions would be appreciated!
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Yang Shi •
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Furthermore, if there is no control sample, e.g. ACC (TCGA), how to get the normalised count from row count?
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Yang Shi •
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