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User: cats_dogs

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Posts by cats_dogs

<prev • 6 results • page 1 of 1 • next >
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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 days ago by cats_dogs0
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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 5 days ago by cats_dogs0 • updated 5 days ago by Peter Langfelder1.7k
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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 19 days ago by cats_dogs0 • updated 19 days ago by Michael Love21k
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Comment: C: Calling svaseq() multiple times
... Okay, thank you! I appreciate the conceptual check. Cheers! ...
written 9 months ago by cats_dogs0
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Comment: C: Calling svaseq() multiple times
... Thanks for your response, Ryan! I was trying to iterate to convergence. I saw this post and got ideas: https://support.bioconductor.org/p/59700/ I realize that svaseq() and duplicateCorrelation() don't do the same thing and that the resulting pvalues might mean "less" with regard to the original di ...
written 9 months ago by cats_dogs0
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Calling svaseq() multiple times
... Hi all, Is it appropriate to call svaseq() multiple times and then only bind the last resulting surrogate variable to the design matrix in edgeR? Our samples are really messy, having been collected from plants grown in different greenhouses, during different seasons, etc, which were inescapable co ...
limma edger sva svaseq written 9 months ago by cats_dogs0 • updated 9 months ago by Ryan C. Thompson7.2k

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