User: endrebak85

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endrebak8510
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Posts by endrebak85

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Run windowCounts only on annotated regions?
... Thanks, csaw is wonderful. ...
written 3 months ago by endrebak8510
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Run windowCounts only on annotated regions?
... I want to run windowCounts only on some annotated regions. Is this possible? readParams has a discard-option, but not one for include... Thanks.  ...
csaw written 3 months ago by endrebak8510 • updated 3 months ago by Aaron Lun14k
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Comment: C: edgeR::estimateDisp gives Error in qr.default(x) : NA/NaN/Inf in foreign functio
... Thanks for the reply. I did need an intercept :) ...
written 3 months ago by endrebak8510
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Answer: A: edgeR::estimateDisp gives Error in qr.default(x) : NA/NaN/Inf in foreign functio
... My design matrix is wrong. The first column should be rownames, not a data column. ...
written 3 months ago by endrebak8510
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edgeR::estimateDisp gives Error in qr.default(x) : NA/NaN/Inf in foreign function call (arg 1) (minimal working example included)
... ​require(edgeR) # edgeR_3.12.1 counts = "Sample1 Sample2 Sample3 Sample4 1 14 19 38 39 2 18 22 38 37 3 23 29 35 41 4 24 34 37 39 5 22 37 40 41" design = "Name Sample 1 Sample1 1 2 Sample2 1 3 Sample3 0 4 Sample4 0" totals = c(9490840, 9491499, 9483062, 9488195) counts.df = read.table(text=count ...
edger estimatedisp written 3 months ago by endrebak8510
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Comment: C: csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
... It did not work. I'll try different things to get it to work, but suggestions welcome :) ...
written 7 months ago by endrebak8510
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Answer: A: csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
... I changed crunch2bam to the following:   crunch2BAM<-function(sam.files, dir=".") # This crunches a set of SAM files to sorted & indexed BAM files using the samtools command. # We avoid calling Rsamtools because of strange errors with 'invalid cross-device link'. I # think it's putting thi ...
written 7 months ago by endrebak8510
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Comment: C: csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
... I do not get e-mail notifications from support.bioconductor, so I did not see your q. Will find out now and report back to you. ...
written 7 months ago by endrebak8510
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Comment: C: csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
... Also, thanks for making the simulations available. For a non-statistician like me, seeing what is produced is much more helpful than reading a description :) ...
written 7 months ago by endrebak8510
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Comment: C: csaw autosim.R: Error in crunch2BAM(fnames): failed to sort BAM file
... Thank you! If I e-mail you directly, my question and your answer will not be googleable for others. Is asking about the paper on the csaw github an acceptable compromise? ...
written 7 months ago by endrebak8510

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Scholar 3 months ago, created an answer that has been accepted. For A: edgeR::estimateDisp gives Error in qr.default(x) : NA/NaN/Inf in foreign functio

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