User: shintzen

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shintzen0
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Posts by shintzen

<prev • 8 results • page 1 of 1 • next >
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Remove any rows with 0 count in S4
... I have run >dds <- DESeqDataSet(se, design = ~ Cal+ Cal:Time + Cal:Cell + Time + Time:Cell + Cell) And dds has some rows with 0 and NAs which is causing issues when I try to take the log2 fold changes >idx.numerator = which(sampleTable$Cell=="4" & sampleTable$Time=="24" & ...
deseq2 s4 written 7 weeks ago by shintzen0 • updated 7 weeks ago by swbarnes290
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DESeqDataSet (dds) assay and sample names
... I want to have sample names from my summarized experiment (se) in my created DESeqDataSet (dds). I would like to look at the counts data in assay(dds) with sample names rather than the numeric headers that exist: > assay(dds) results in: > [,1] [,2] [,3] [,4] [,5] [,6] [,7] [ ...
deseq2 written 7 weeks ago by shintzen0 • updated 7 weeks ago by Michael Love22k
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Error in nbinomLRT while trying to follow time course analysis
... I am trying to understand what this error means: Error in nbinomLRT(object, full = full, reduced = reduced, quiet = quiet, : less than one degree of freedom, perhaps full and reduced models are not in the correct order I am following https://www.bioconductor.org/packages/devel/workflows/vignettes/r ...
deseq2 written 7 weeks ago by shintzen0 • updated 7 weeks ago by Michael Love22k
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Comment: C: Unable to find an inherited method for function 'results' for signature '"DESeqD
... This worked, I didn't notice a package masking it on load. Do you have any resources to share about packages that get masked? I would like to know how to prevent this ...
written 8 weeks ago by shintzen0
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Comment: C: Unable to find an inherited method for function 'results' for signature '"DESeqD
... I have with library(DESeq2) and there is no issue on load ...
written 8 weeks ago by shintzen0
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Unable to find an inherited method for function 'results' for signature '"DESeqDataSet"'
... I am getting an error about results function not being found. I have run this in days past but I had to restart my computer and now it isn't working. I tried reloading packages with: > source("https://bioconductor.org/biocLite.R") pkgs <- rownames(installed.packages()) biocLite(p ...
deseq2 written 8 weeks ago by shintzen0 • updated 8 weeks ago by Michael Love22k
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DESeq2 standard error estimate (lfcSE)
... I have quite a few results of DESeq2 where the lfcSE is very near to 1. I don't fully understand how I should interpret this value, and though I have read through the first several pages of google with a few different search terms, I am still not confident that I fully understand. From what I've u ...
deseq2 written 10 weeks ago by shintzen0 • updated 10 weeks ago by Michael Love22k
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prepDE KeyError on MSTRG
... I am trying to run prepDE (found here http://ccb.jhu.edu/software/stringtie/dl/prepDE.py) however I am getting an error that does not give me a lot of information on what exactly the issue is or where to look on where to solve it. I googled but didn't find much.  C:\Python27\python.exe prepDE.py -i ...
deseq2 prepde written 3 months ago by shintzen0 • updated 3 months ago by Michael Love22k

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