User: Alexandre Kuhn

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3 months ago
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6 years, 11 months ago
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Posts by Alexandre Kuhn

<prev • 6 results • page 1 of 1 • next >
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Answer: A: wrong output of DNAcopy::segment() for chr. with empty copy number data
... It does not seem to be true. segment() handles NAs correctly if there are other, non-NA values on the same chromosome: > segment(CNA(genomdat=c(1,2,1,NA,2,3),chrom=c(rep("chr1",3),rep("chr2",2),"chr3"),maploc=c(1:3,1:2,1))) Analyzing: Sample.1 Call: segment(x = CNA(genomdat = c(1, 2, 1, NA, ...
written 3 months ago by Alexandre Kuhn20
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wrong output of DNAcopy::segment() for chr. with empty copy number data
... Hello, I encountered a rare problem with segment() in the DNAcopy package. Specifically I see artifactual segments with ouptut$loc.start greater than output$end.start and output$num.mark=0 and output$seg.mean=NA. In my case, it seems to be caused by "chromosomes" (contigs) with empty copy number d ...
dnacopy written 3 months ago by Alexandre Kuhn20
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Answer: A: getReadCountsFromBAM and paired-end reads
... Thanks for your explanations. Could you please provide a pointer to the errors that were reported with the previous "getReadCountsFromBAM" function? It would help me to understand if the counting I did using cn.mops in Bioc 3.3 gave accurate results, as well as maybe provide some ideas on how to r ...
written 5 months ago by Alexandre Kuhn20
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getReadCountsFromBAM and paired-end reads
... Hello Guenter, Thank you for your useful package cn.mops. I use your function "getReadCountsFromBAM". However I noticed that starting from Bioconductor version 3.4, the "mode" argument disappeared (I noticed it as I used to count reads from paired-end sequencing data and setting mode="paired"). T ...
cn.mops written 5 months ago by Alexandre Kuhn20
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Answer: A: GEOsubmission help request
... Hi Marco, you might be missing double quotes around EarlyAdvancedATHERO in this command: > microarray2soft(mysampleID, "sampleInfo.txt", EarlyAdvancedATHERO,"seriesInfo.txt",softname = "AdvEar.soft", expressionmatrix = "EarlyAdvancedATHERO.txt") microarray2soft expect a character vector or a c ...
written 6.6 years ago by Alexandre Kuhn20
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Problems with the package GEOsubission
... Hi Fabian, My apologies for taking so long to respond. In your test, you might not have made the right comparison > sampDat <- read.delim(file.path(dataDir, "dRED.txt")) > expMatrix <- read.delim(file.path(dataDir, "eRED.txt")) > colnames(expDat) == sampDat$Sample_supplementary_fil ...
microarray written 6.9 years ago by Alexandre Kuhn20 • updated 6.9 years ago by Fabian Grammes30

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