User: Arnaud Amzallag

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Posts by Arnaud Amzallag

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Comment: C: Standard error and effect size from Limma
... I'd say, `(CI.R - CI.L)/3.92` (since the 95% confidence intervals should be plus/minus 1.96se) ...
written 3.6 years ago by Arnaud Amzallag100
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justRMA (package Affy) messing up phenoData when passing an AnnotatedDataFrame
... Hello to all, I think there is a problem with a certain call of justRMA (see below); it mixes the sample names of pData but keeps the annotation the same, effectively miss labeling samples without returning a single error or warning. > phenoData <- read.AnnotatedDataFrame(paste(prodir, "samp ...
annotation cancer written 5.6 years ago by Arnaud Amzallag100 • updated 5.6 years ago by James W. MacDonald51k
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Answer: A: subset GRanges object via ElementMetadata
... test.gr[values(test.gr)$over %in% 2] works. test.gr[values(test.gr)$over == 2] works too if over does not contains NAs. Arnaud On Feb 22, 2013, at 10:33 AM, Hermann Norpois wrote: > Hello, > > I am looking for a method to subset a GRangesObject by means of values (or > ElementMetada ...
written 6.7 years ago by Arnaud Amzallag100
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IRanges: Request for a "step" argument in runsum
... Hello Hervé and Michael, On Jun 29, 2011, at 6:29 PM, Michael Lawrence wrote: > > > 2011/6/28 Hervé Pagès > Hi Michael, Arnaud, > > > On 11-05-25 08:21 AM, Arnaud Amzallag wrote: > Thank you Michael, > > for some email filters reasons I saw your reply only now. > ...
coverage annotation cancer process iranges genomes written 8.3 years ago by Arnaud Amzallag100 • updated 8.3 years ago by Hervé Pagès ♦♦ 14k
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rtracklayer Rle to bigWig (export.bw ?)
... Hello to all, I am trying to make a bigWig for loading in UCSC from a SimpleRleList. I cannot find an exemple so I just tried, but I get an error (Error in is.null(genome) : 'genome' is missing). If someone could send me the correct code for this (if this is implemented at all) that would be nice. ...
written 8.3 years ago by Arnaud Amzallag100
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rtracklayer Rle to bigWig (export.bw ?)
... Hello to all, I am trying to make a bigWig for loading in UCSC from a SimpleRleList. I cannot find an exemple so I just tried, but I get an error (Error in is.null(genome) : 'genome' is missing). If someone could send me the correct code for this (if this is implemented at all) that would be nice. ...
written 8.3 years ago by Arnaud Amzallag100
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Comment: C: IRanges: Request for a "step" argument in runsum
... Thank you Michael, for some email filters reasons I saw your reply only now. I recon that in my case that would have been much smoother if sum() would call viewSums() by default and I agree that "It's more intuitive to think of an RleViews like an RleList rather than an IntegerList.". I would supp ...
written 8.4 years ago by Arnaud Amzallag100
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Comment: C: IRanges: Request for a "step" argument in runsum
... Thank you Michael, the function viewSums was exactly what I needed ! 0.014 seconds for viewSums(Views(myrle, ir)) vs 54 seconds for sum(Views(myrle, ir)) on chr22, one sample. I use this now instead of of runsum, no problem of memory, and probably even faster. for full the genome on many samples th ...
written 8.5 years ago by Arnaud Amzallag100
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IRanges: Request for a "step" argument in runsum
... Dear IRanges developers, runsum is a very fast and convenient function to compute on Rle coverages, for instance. However when it is run on several chromosomes and several samples, it can get very memory intensive. For instance on human chromosome 1, it outputs a vector of length 250 millions, so f ...
cancer iranges genomes written 8.5 years ago by Arnaud Amzallag100 • updated 8.5 years ago by Michael Lawrence11k
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Comment: C: find overlap of bed files of different length
... Thank you for your help Michael. I might ask them how they mapped it, I guess they had some coordinates for the Entrez genes and overlapped them with the transcripts. Arnaud On 4 févr. 11, at 18:11, Michael Lawrence wrote: > There's a table that maps the UCSC ID's to Entrez Gene. Called > ...
written 8.7 years ago by Arnaud Amzallag100

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