User: Hamid Bolouri

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Posts by Hamid Bolouri

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Comment: C: error running ChAMP vignette example
... Wow, that was quick! Thanks Dan. --H ...
written 21 months ago by Hamid Bolouri90
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error running ChAMP vignette example
... hi; I get: Error in sort(abs(diff(genomdat)))[1:n.keep] :   only 0's may be mixed with negative subscripts running ChAMP's vignette example. Details below. Could anyone suggest a fix? Thanks Hamid # code, stdout, traceback() and sessionInfo() follows: library(ChAMP) library(ChAMPdata) data(t ...
champ software error written 21 months ago by Hamid Bolouri90
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package 'ChAMP' demo/test code fails at champ.CNA()
... hi; Running the 'ChAMP' demo with its test data per vignette instructions ending with : champ.process(directory = testDir) all seems to work until this happens: --- Preparing files for ComBat Your data is being logit transformed before batch correction Beginning batch correction Found 3 batches ...
software error written 2.8 years ago by Hamid Bolouri90 • updated 10 months ago by Yuan Tian70
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Answer: A: getNearestTSS in FDb.InfiniumMethylation.hg19_2.0.10 ?
... That did it!  Thanks for the super-quick response. Hamid   ...
written 3.0 years ago by Hamid Bolouri90
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getNearestTSS in FDb.InfiniumMethylation.hg19_2.0.10 ?
... hi; I am trying to use 'getNearestTranscript' and 'getNesrestTSS' for annotation of 450K DNA-me array data as in the ref. manual, but I get: > ?getNearestTranscript No documentation for âgetNearestTranscriptâ in specified packages and libraries: you could try â??getNearestTranscriptâ>  ?getN ...
software error written 3.0 years ago by Hamid Bolouri90
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'RmiR.Hs.miRNA' DB versions and filtering criteria?
... hi; I am wondering what versions of: "miranda","mirbase","mirtarget2","pictar","tarbase","targetscan" are provided by the current version of 'RmiR.Hs.miRNA'. Also, were the above DBs filtered in any way? (A similar query in 2011: https://stat.ethz.ch/pipermail/bioconductor/2011-May/039352.html ...
written 4.1 years ago by Hamid Bolouri90
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Comment: C: VariantAnnotation development branch issue
... Thanks very much for the quick diagnosis & fix Martin. Will do. Hamid ----- Original Message ----- From: "Martin Morgan" To: "Steve Lianoglou" Cc: "Hamid Bolouri" , bioconductor at r-project.org Sent: Monday, November 5, 2012 8:30:13 PM Subject: Re: [BioC] VariantAnnotation development branc ...
written 5.0 years ago by Hamid Bolouri90
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VariantAnnotation development branch issue
... hi : I am finding that the development version of R with VariantAnnotation_1.5.7 runs fine on one PC but not on another with very similar hardware and configuration: > fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools", + mustWork=TRUE) > tbx <- TabixFi ...
written 5.0 years ago by Hamid Bolouri90 • updated 5.0 years ago by Steve Lianoglou12k
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Comment: C: "graphite" Biocarta 'native' graphs different from Biocarta web site?
... It works! Thanks very much indeed Laurent. Best wishes; Hamid ----- Original Message ----- From: "laurent jacob" To: "Hamid Bolouri" Cc: bioconductor at r-project.org Sent: Friday, June 8, 2012 1:30:35 PM Subject: Re: [BioC] DEGraph graph format? Hi Hamid, 2012/6/7 Hamid Bolouri : >>l ...
written 5.5 years ago by Hamid Bolouri90
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Answer: A: "graphite" Biocarta 'native' graphs different from Biocarta web site?
... hello; Can anyone tell me how to use DEGraph with the pathways in NCIGraphData? The DEGraph Demo: >data("Loi2008_DEGraphVignette", package="DEGraph") >classData <- classLoi2008 >exprData <- exprLoi2008 >annData <- annLoi2008 >grList <- grListKEGG >res <- testOneGr ...
written 5.5 years ago by Hamid Bolouri90

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