Moderator: Rafael A. Irizarry

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Posts by Rafael A. Irizarry

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Postdoc Position
... Hi all! See below. Please email me if you are interested. -r Postdoctoral Fellowship in Biostatistics and Epigenomics at Johns Hopknis University The Departments of Medicine and Biostatistics at Johns Hopkins University are inviting applications for positions at the level of Postdoctoral Fellow. ...
genetics written 11.7 years ago by Rafael A. Irizarry2.3k
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Comment: C: Fwd: MAS5+32, PLIER+16 alorithms reported in affycomp
... to avoid dividing by numbers close to 0. earl added 16 to the PLIER expression values (before log!) and 32 to the MAS 5.0 ones. On Mon, 6 Mar 2006, James W. MacDonald wrote: > Frank Duan wrote: >> Hi All, >> >> Sorry to raise up this question again. I did search the forum but ...
written 11.7 years ago by Rafael A. Irizarry2.3k
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Sales
... Does anybody know how one can get an estimate of the number of arrays, say, Affymetrix and Agilent have sold? ...
written 11.7 years ago by Rafael A. Irizarry2.3k • updated 11.7 years ago by Paul Grosu110
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Comment: C: advice on Biostrings
... thanks everybody. this made it much faster: tmpseq <- DNAString(pmseq) GC <- DNAString("GC") CG <- DNAString("CG") tmp <- sapply(1:length(tmpseq),function(i){ y=tmpseq[i] c(alphabetFrequency(y)[2:5], length(matchDNAPattern(GC,y)), length(matchDNAPattern(CG,y))) }) Martin Mo ...
written 11.7 years ago by Rafael A. Irizarry2.3k
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advice on Biostrings
... hi im using biostrings to count base content as well as pair of bases content. im using the following sniped of code: ###pmseq is a vector of character strings (not of the same nchar). tmp <- sapply(pmseq,function(x){ y = DNAString(x) c(alphabetFrequency(y)[2:5], ##count A,T,G,C length( ...
biostrings written 11.8 years ago by Rafael A. Irizarry2.3k • updated 11.8 years ago by Martin Morgan ♦♦ 20k
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Answer: A: Order of probesets in an exprSet
... fortuitous. look at indexProbes. we use whatever order ls gives us. -r On Mon, 7 Nov 2005, Jamain, Adrien J wrote: > Dear BioC people, > > I have a little technical question about how the order of the probesets > in an exprSet is defined. > Is this order given by the order of the ...
written 12.0 years ago by Rafael A. Irizarry2.3k
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Answer: A: makepackage of affy's 100K and 500K SNP chip
... the oligo and makePlatformDesign packages handle these chips. they are in devel stages (and thus available in the devel section of bioc) so testers are welcomed. On Thu, 27 Oct 2005, Zhang, Jacob wrote: > Hello, bioconductor developers: > > Are there any one working on to make bioconduc ...
written 12.1 years ago by Rafael A. Irizarry2.3k
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Comment: C: gpr.gz
... yes, but then i need to hack the existing parsers. maybe instead of just me doing it, the maintainer(s) can do it for everybody? see Sean's email for what he suggests. -r On Thu, 13 Oct 2005, Robert Gentleman wrote: > Hi, > Does gzfile not do what you want? > > > apropos("gz") ...
written 12.1 years ago by Rafael A. Irizarry2.3k
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gpr.gz
... hi! any recs on how to deal with gzipped gpr files? if possible id like to read them into bioc without unzipping them first. -r ...
written 12.1 years ago by Rafael A. Irizarry2.3k • updated 12.1 years ago by rgentleman5.5k
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Comment: C: Please Help on how to install Mapping10K_XBa142 in R.
... karsper is correct about oligo and makePlatformDesign. affy wont handle these data. with oligo you will be able to read in data and look at probe level intensities. you can write your own scripts to analyze this data. in a month or two we will add functionality to make calls and do copy number anal ...
written 12.2 years ago by Rafael A. Irizarry2.3k

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