User: yk.gatc

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yk.gatc0
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Posts by yk.gatc

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Comment: C: DESeq2 LFC shrinkage is for designs with interactions
... lfcShrink with "normal" and "apeglm" gives different volcano patterns (please see image attached). Is this expected behavior of different types of shrinkage methods? Or is it something odd here? https://imgur.com/a/N4Wwp ...
written 9 months ago by yk.gatc0
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Comment: C: DESeq2 LFC shrinkage is for designs with interactions
... With the new code (developer version), lfcShrink estimation was done successfully with the following message  - > resLFC <- lfcShrink(dds, coef=22, type="apeglm", res=res) using 'apeglm' for LFC shrinkage Some rows did not converge in finding the MAP [1] DESeq2_1.19.36 apeglm_1 ...
written 10 months ago by yk.gatc0
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Comment: C: DESeq2 LFC shrinkage is for designs with interactions
... I reinstalled the packages from Bioconductor, now I get different errors - > resLFC <- lfcShrink(dds, coef=22, res=res, type="apeglm") using 'apeglm' for LFC shrinkage Error in solve.default(o$hessian) : system is computationally singular: reciprocal condition number = 1.16041e-129 In addi ...
written 10 months ago by yk.gatc0
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Comment: C: DESeq2 LFC shrinkage is for designs with interactions
... Thank you Michael for your time and support.  Btw, I am getting an error when I try to apply apeglm method -  res2 <- lfcShrink(dds, coef = 22, type = "apeglm", res = res) using 'apeglm' for LFC shrinkage Error in apeglm::apeglm(Y = Y, x = design, log.lik = log.lik, param = disps, : unus ...
written 10 months ago by yk.gatc0
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Comment: C: DESeq2 LFC shrinkage is for designs with interactions
... Thanks for the suggestions. But with the design I am using, I cannot use coef argument with type="apeglm" to shrink LFC values. My objective here is to compare two treatment groups (with matched controls) which I supply as contrast=list(condA,condB). Do you have any suggestions to apply LFC shrinka ...
written 10 months ago by yk.gatc0
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Comment: A: DESeq2 LFC shrinkage is for designs with interactions
... Thanks Michael for the quick response.  I did try "ashr" method, but it gave me the following warning -  > resultsNames(dds) [1] "Intercept" "grp_Y_vs_X" "grpX.ind.n10" "grpY.ind.n10" "grpX.ind.n2" [6] "grpY.ind.n2" "grpX.ind.n3" "grpY.ind.n3" "grpX.ind.n4" "grpY.ind.n4" [11] "grpX. ...
written 11 months ago by yk.gatc0
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DESeq2 LFC shrinkage is for designs with interactions
... Hi, It seems like LFC shrinkage is not implemented for designs with interactions. Is there a way to get shrinked LFC values for designs with interactions? DESeq2_1.19.14 Thanks, YK ...
deseq2 lfcshrink written 11 months ago by yk.gatc0

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