hgu133a : probe ids to gene symbols
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.9 years ago
Hi, I was processing some data and wanted to consolidate expression values by gene, instead of by probe id as given the expression dataset. The hgu133a chips has 22283 probe ids corresponding to 12704 genes. Is there any function in the package that will automatically consolidate the expression value genewise? In other words (from the code given below), how can I get a 12704 X 38 matrix from the probe level 22283 X 38 matrix? > dim(emat) # expression data for 22283 probes and 38 samples [1] 22283 38 > probes <- rownames(emat) > gs <- unlist(mget(probes,hgu133aSYMBOL)) > length(probes) [1] 22283 > length(unique(gs)) [1] 12704 many thanks! [[alternative HTML version deleted]]
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@sean-davis-490
Last seen 12 weeks ago
United States
On Thu, Mar 4, 2010 at 6:00 PM, Tim Smith <tim_smith_666 at="" yahoo.com=""> wrote: > Hi, > > I was processing some data and wanted to consolidate expression values by gene, instead of by probe id as given the expression dataset. The hgu133a chips has 22283 probe ids corresponding to 12704 genes. Is there any function in the package that will automatically consolidate the expression value genewise? In other words (from the code given below), how can I get a 12704 X 38 matrix from the probe level 22283 X 38 matrix? Hi, Tim. Have a look at the findLargest() function in the genefilter package. Sean >> dim(emat) ?# expression data for 22283 probes and 38 samples > [1] 22283 ? ?38 > >> probes <- rownames(emat) >> gs <- unlist(mget(probes,hgu133aSYMBOL)) >> length(probes) > [1] 22283 > >> length(unique(gs)) > [1] 12704 > many thanks! > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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