affy 1.1 version
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Isaac Neuhaus ▴ 360
@isaac-neuhaus-22
Last seen 8.8 years ago
United States
Why is the affy version in the developmental packages 1.1 now? A couple of months ago it was 1.2
affy affy • 894 views
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Laurent Gautier ★ 2.3k
@laurent-gautier-29
Last seen 9.6 years ago
On Wed, Nov 20, 2002 at 11:39:00AM -0500, Isaac Neuhaus wrote: > Why is the affy version in the developmental packages 1.1 now? A couple > of months ago it was 1.2 > Dear Isaac, The version numbering was subject to a floating policy up to a very recent time (and the decision that the new release for BioC would be 1.1). The version number has probably been changed to match that (I assume...) The version 1.1 of affy is both the released and developmental version for the moment. Laurent
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Hi all! Can someone explain to my why the hist function applied to the expression values returns less values, i.e. less genes, than there are on the hu68 chip? Here my code fragments: > Mydata <- ReadAffy(CDFfile="hu6800.cdf",...) > Mydata.rma <- express(Mydata) > dim(exprs(Mydata.rma)) [1] 7129 18 # ok, here we have 7129 expression values > Mydata.rma.hist <- hist(exprs(Mydata.rma),,plot=F) > sum(Mydata.rma.hist$counts) [1] 42774 # here we are down to 42774 genes Cheers, Hinnerk
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Hi Hinnerk, what's length(whichis.na(exprs(Mydata.rma)))) respectively length(which(!is.na(exprs(Mydata.rma)))) ??? Best regards Wolfgang Huber w.huber@dkfz.de http://www.dkfz.de/abt0840/whuber Tel +49-6221-424709 Fax +49-6221-42524709 DKFZ, Division of Molecular Genome Analysis 69120 Heidelberg, Germany -----Original Message----- From: bioconductor-admin@stat.math.ethz.ch [mailto:bioconductor-admin@stat.math.ethz.ch]On Behalf Of Hinnerk Boriss Sent: Thursday, November 21, 2002 11:21 AM To: 'Bioconductor' Subject: [BioC] data reduction in "hist" function? Hi all! Can someone explain to my why the hist function applied to the expression values returns less values, i.e. less genes, than there are on the hu68 chip? Here my code fragments: > Mydata <- ReadAffy(CDFfile="hu6800.cdf",...) > Mydata.rma <- express(Mydata) > dim(exprs(Mydata.rma)) [1] 7129 18 # ok, here we have 7129 expression values > Mydata.rma.hist <- hist(exprs(Mydata.rma),,plot=F) > sum(Mydata.rma.hist$counts) [1] 42774 # here we are down to 42774 genes Cheers, Hinnerk _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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Hi Wolfgang! > length(whichis.na(exprs(Mydata.rma)))) returns: 0 > length(which(!is.na(exprs(Mydata.rma)))) returns: 128322 which is just three times sum(Mydata.rma.hist$counts) = 42774. Why???? Does that help? Best, Hinnerk > > > Hi all! > > Can someone explain to my why the hist function applied to the > expression values returns less values, i.e. less genes, than there are > on the hu68 chip? > > Here my code fragments: > > > Mydata <- ReadAffy(CDFfile="hu6800.cdf",...) > > Mydata.rma <- express(Mydata) > > dim(exprs(Mydata.rma)) > [1] 7129 18 > # ok, here we have 7129 expression values > > > Mydata.rma.hist <- hist(exprs(Mydata.rma),,plot=F) > > sum(Mydata.rma.hist$counts) > [1] 42774 > # here we are down to 42774 genes > > Cheers, > Hinnerk > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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