Hi, all： I want to use TCGA's RNA-seq data for cox analysis, but the results calculated using FPKM are not the same as those calculated using TPM. I would like to ask which one is correct ？or， I am doing something wrong？
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It makes sense that you would obtain different results from FPKM and TPM. Neither of these are optimal for the purposes of statistical modelling.
I would encourage you to obtain the TCGA raw counts and then re-normalise using DESeq2. Then transform the normalised 'counts' via the regularised log transformation with blind=FALSE. It is on those regularised log expression levels that you would perform your Cox regression analysis.
Edit: the variance-stabilised expression levels would be fine, too.
Kevin
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