User: john.hu

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Posts by john.hu

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Comment: C: DESeq2 contrast cleaning problem
... Yeah, I think this function is written for expanded matrix only. For standard matrix, the filter works file when a contrast is specified in text as contrast=c("Term", "A", "B")  It makes biological sense to reset the log2fc and p-values for RNA-Seq data when all samples in the contrast have zero co ...
written 3.5 years ago by john.hu0
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DESeq2 contrast cleaning problem
... I am testing DESeq2 1.10.1 version and find some issue with cleanContrast function. I use a standard 2x2  A*B design with interaction terms.  DESeqDataSetFromMatrix(countData = round(datacounts), colData = designtable, design = ~ Gender*Site) dds<- DESeq(dds, modelMatrixType="standard") outpu ...
deseq2 bugs software error written 3.5 years ago by john.hu0 • updated 3.5 years ago by Michael Love24k

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