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mskcc / RNAseqDB

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about performing DEGs analysis #13

Open yan911 opened 3 years ago

yan911 commented 3 years ago

Can I combine the read count that both from TCGA and GTEx, and then perform DEG analysis directly without remove batch effect in your provided count data? Or I can only perform DEG analysis via DESeq2/edgeR on the same data set source? The sample workflow is below: GTEx normal count + TCGA normal +tumor count without remove batch ---> DESeq2/edgeR Or can only : TCGA normal count + TCGA tumor count ---> DESeq2/edgeR

thanks for your explanation

JiahuaQu commented 1 year ago

I also have the similar question: If I only have normal sample data in GTEx and only tumor sample data in TCGA, can I analyze GTEx normal count + TCGA tumor count? It even looks strange to remove the batch effect in this case, because the batch effect derived from using different databases is always together with the effect from normal or tumor samples.