User: Cece

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Cece0
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Posts by Cece

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Comment: C: DESeq2 error with lfcshrink for interaction term
... Sorry Michael, That was a typo. DESeq should have been DESeqDataSetFromMatrix(countdata...) to set up my dds_full object. ...
written 11 weeks ago by Cece0
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Comment: C: DESeq2 error with lfcshrink for interaction term
... Hi Michael, I eventually simplified my design to run: dds_full <- DESeq(countData = mycounts, colData=merge2, design= ~ Age + group + Cov1 + Cov2) dds_red <-DESeq(dds_full, test = "LRT", reduced = ~ Age + group + Cov1) So I just want to be certain that under these conditions, I'm lo ...
written 11 weeks ago by Cece0
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Comment: C: DESeq2 error with lfcshrink for interaction term
... So if I understand correctly, if my full design looks like this: ds <- DESeqDataSetFromMatrix(countData = mycounts, colData=merge2, design= ~ Age + Gender + Cov3 + Cov2 + Cov1 + Condition + Cov1:Condition + Cov2:Condition + Cov3:Condition) then I can test the e ...
written 9 months ago by Cece0
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DESeq2 error with lfcshrink for interaction term
... Hi All, 1.   I'm trying to use the code below to shrink the LFCs in my model but I keep generating an error. resLFCint <- lfcShrink(dds, res = res, name="Cov1.Conditioncase", type="apeglm")) using 'apeglm' for LFC shrinkage Error: !missing(coef) is not TRUE design ~ Age + Gender + Cov3 + Cov2 ...
deseq2 interaction term written 9 months ago by Cece0 • updated 9 months ago by Michael Love24k

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