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Posts by mdidish
... Thank you for your response. But by adding batch to the design, I still have a strong batch effect when I plot PCA with DESeq matrix. So I can't use these matrix to clustering tumors. When I remove batch effect with ComBat, I have very good results very good result on PCA plot, but I can't use ComB ...
... Hi I would like to correct batch effect using deseq2, to analyze one hundred of RNA-Seq of tumors, without experimental design. 80 tumors were sequenced in 2018, and 20 in 2019; I can see a strong batch effect whent I plot PCA on reads count or on data after DESeq between 2018 and 2019 tumors. Usu ...
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