User: Misha Kapushesky

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Posts by Misha Kapushesky

<prev • 13 results • page 1 of 2 • next >
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Answer: A: poor precision of matrix inverse?
... Try solve(b) %*% b. --Misha On Mon, 22 Nov 2010, zack liu wrote: > Dear members, > > I am using "solve" to compute the inverse of a 5 by 5 matrix using R and > matlab. The results are quite interesting.. It seems that R has very poor > precision in terms of calculating inverse of ...
written 8.6 years ago by Misha Kapushesky130
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Comment: C: Fastest way to read CSV files
... Hi, Martin is absolutely right. For our data analysis needs here we use NetCDF extensively. It's about as fast as direct binary reads, is portable, etc., without the headache of worrying about many nitty gritty details. --Misha > data) and robust. Also SQL, NetCDF and friends which will be por ...
written 8.8 years ago by Misha Kapushesky130
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Comment: C: Fastest way to read CSV files
... Hi, If you did do this in binary, we'd see the following: > x <- matrix(floor(runif(1.7e6 * 20)*1000),nr=20) > z <- writeBin(as.vector(x),file("test.bin","wb")) > system.time({zz <- readBin(file("test.bin","rb"),numeric(),20*1700000); dim(zz) <- c(20,1700000)}) user syst ...
written 8.8 years ago by Misha Kapushesky130
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Comment: C: 'Rsamtools' produces segfaults with XS tag
... Hi, Thanks for the speedy fix! --Misha On Fri, 13 Aug 2010, Martin Morgan wrote: > On 8/13/2010 2:11 PM, Misha Kapushesky wrote: >> Hi, >> >> I put it on http://www.ebi.ac.uk/~ostolop/accepted_hits.sortednames.bam. >> After some more tinkering - it seems I can't reprod ...
written 8.9 years ago by Misha Kapushesky130
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Comment: C: 'Rsamtools' produces segfaults with XS tag
... Hi, I put it on http://www.ebi.ac.uk/~ostolop/accepted_hits.sortednames.bam. After some more tinkering - it seems I can't reproduce this on my Mac, only on our Linux install. I also just noticed that the released version is 1.0.7, while we seem to have 1.1.11, and yet our R is 2.11.1 - perhaps it's ...
written 8.9 years ago by Misha Kapushesky130
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Answer: A: 'Rsamtools' produces segfaults with XS tag
... Hi, I can add more detail to this - the same problem: > library( "Rsamtools" ) ... > tags <- c("NM", "MD", "XA", "XS","NS") > and_file = "SRR034792/tophat_out/accepted_hits.sortednames.bam" > and_bam = scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE ...
written 8.9 years ago by Misha Kapushesky130
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Comment: C: regarding package ArrayExpress
... Hi, Without tweaking read.table, you'd have to read row names as one of the data columns, then make.names on that set of names and set the row names to the modified ones. So, something like d <- read.table("foo.tab") ## if read.table("foo.tab", row.names=1) fails rownames(d) <- make.names(d ...
written 9.8 years ago by Misha Kapushesky130
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Comment: C: Expressionset from ArrayExpress processed data
... Hi, Audrey (the author of the ArrayExpress package) will probably be able to give a more precise answer, but I believe a capacity for the this package to return ExpressionSet objects from processed data in AE is planned and such an implementation may be available in the development branch (check bi ...
written 10.4 years ago by Misha Kapushesky130
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Comment: C: Reading Agilent files using read.maimages
... Dear Steve et al, The files you downloaded from ArrayExpress are in fact in its own format. For this experiment, in case you might find it useful, we placed the original Agilent raw data files as given to us by the submitter at ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/ experiment/MEXP/E-ME ...
written 11.9 years ago by Misha Kapushesky130
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Limma - small bug in decideTests?
... Dear List, I looked through the archives and didn't notice anyone pointing this out, so I thought I'd ask: If decideTests() is called with the method argument set to hierarchical (by the way, that word is misspelled in the implementation as 'heirarchical' - if someone should call it with correct s ...
written 12.0 years ago by Misha Kapushesky130

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