User: cats_dogs

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cats_dogs20
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Posts by cats_dogs

<prev • 13 results • page 1 of 2 • next >
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Comment: C: DESeq2 for QuantSeq data
... Oh yeah, you should trim off the adapters and do QC, if that wasn't clear. You can do that in R, but you don't have to. ...
written 11 weeks ago by cats_dogs20
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WGCNA: net$colors and module colors don't match up; module assignments are different
... Hi all, I have run `blockwiseConsensusModules()` [on my data][1], and the resulting list contains a list of colors per gene. When making the module-trait correlation table, module colors are assigned thus in the tutorial: MEColors = labels2colors(as.numeric(substring(names(net$multiMEs[[1]]$d ...
wgcna written 12 weeks ago by cats_dogs20
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Answer: A: DESeq2 for QuantSeq data
... There's nothing about this particular bioinfo workflow that is QuantSeq specific (though Hisat2 is now generally recommended over Tophat2). Yes, you can use DESeq2 on QuantSeq data. ...
written 12 weeks ago by cats_dogs20
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Comment: C: WGCNA: consensusTOM() doesn't save TOMs & returns setNames error (but sets are n
... Ah yeah, it was a discrepancy in my .profile. Fixed now and the function works - thanks so much for your help! ...
written 3 months ago by cats_dogs20
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Comment: C: WGCNA: consensusTOM() doesn't save TOMs & returns setNames error (but sets are n
... I think I may have found the issue: The function in consensusTOM.R in the [documentation][1] seems to pass 18 arguments to tomSimilarity_call in [networkFunctions.c][2], but in the updated version, it passes 19 arguments .Call("tomSimilarity_call", data, weights, as.integer(C ...
written 3 months ago by cats_dogs20
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Comment: C: WGCNA: consensusTOM() doesn't save TOMs & returns setNames error (but sets are n
... Thanks so much for the quick response! I downloaded and installed 1.66; it's running now, and I'll update this post when the job finishes, likely tomorrow. quick edit: It killed the function with Error in .Call("tomSimilarity_call", selExpr, selWeights, as.integer(CcorType), : Incorr ...
written 3 months ago by cats_dogs20
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WGCNA: consensusTOM() doesn't save TOMs & returns setNames error (but sets are named)
... Hi all, For context, I'm still working on the dataset about which I raised [this question][1]. Running consensusTOM() results in neither the calibrated nor consensus TOMs being saved to disk/returned to the workspace and throws this error: Error in .processFileName(calibratedIndividualTOMFile ...
wgcna written 3 months ago by cats_dogs20 • updated 3 months ago by Peter Langfelder2.1k
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Comment: C: WGCNA - confounding effect based on technical variables (some continuous)
... Hi Dr. Langfelder, Thank you for your response! Initially, I had split up the analysis by genotype, where I noticed that timepoints 1 and 3 had unrealistically similar eigenegene correlations, like this. I estimate that ~70% of the modules had such an association. ![timepoints 1 and 3 have simil ...
written 4 months ago by cats_dogs20
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WGCNA - confounding effect based on technical variables (some continuous)
... Hi all, I am running WGCNA on a set of 129 samples from three timepoints with three diseases and various physiological traits. Unfortunately, due to project logistics, they were not able to be sequenced at the same time, and looking at the module-trait relationship, it looks like there is quite a s ...
wgcna batch effect continuous written 4 months ago by cats_dogs20 • updated 4 months ago by Peter Langfelder2.1k
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DESeqFromMatrix for 3'end data via tximport; non-integer values
... Hi all, My 3' QuantSeq counts matrix has been summarized and imported with tximport (txi$counts) and contains non-integer values, causing problems with DESeqDataSetFromMatrix. Code: txi <- tximport(files = files, type="salmon", tx2gene = transcripts, countsFromAbundance = "no") target ...
deseq2 tximport written 4 months ago by cats_dogs20 • updated 4 months ago by Michael Love24k

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