User: Rob Dunne

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Rob Dunne230
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Posts by Rob Dunne

<prev • 23 results • page 1 of 3 • next >
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Answer: A: is it possible to find sample batch # in CEL files?
... Hi Brian, affxparser has a function called readCelHeader. library(affxparser) dates<-rep(0,length(files)) for (i in 1:length(files)){ datheader<-readCelHeader(ff[i])$datheader dd<-gsub(".*([0-9]{2,2}/[0-9]{2,2}/[0-9]{2,2}).*","\\1", datheader) dates[i]<-dd ...
written 6.6 years ago by Rob Dunne230
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Comment: C: bout big data set for Affy R packge
... Hi Benilton, Unless I am missing something, ff wont help in this case. From the ff help page "Currently ff objects cannot have length zero and are limited to ?.Machine$integer.max? elements" and .Machine$integer.max is 2^(31)-1. This is exceeded when you try to load 328 Affy exon arrays hence l ...
written 6.7 years ago by Rob Dunne230
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Answer: A: bout big data set for Affy R packge
... Hi Wei Liu, if they are affymetrix 1.0 ST exon arrays, I can send you a modified version of read.celfiles from the oligo package that should read a 300 microarray data set. I dont know it it will work for other array types, possibly not without some work. It is a modified version of the read.celfi ...
written 6.7 years ago by Rob Dunne230
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Comment: C: oligo package
... Hi List, I am having a problem reading HuGene 1.0 arrays with the oligo package. library(oligo) read.celfiles(filenames=filenames) # Could not open file ~/Downloads/SSA/original/CC_Black_(HuGene-1_0-st-v1).CEL Looking inside read.celfiles, it seems that the problem may start with getCelChipType ...
written 6.8 years ago by Rob Dunne230
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R matrix size limits and array data
... Hi, I am hitting the 2^31-1 limit on array entries in loading and normalizing a set of exon arrays. The oligo package uses "ff" if you have it loaded but ff seems to have the same limit. I have modified some routines from an older version of oligo (1.10.4) to use big.matrix from the big.memory pac ...
oligo written 6.9 years ago by Rob Dunne230 • updated 6.9 years ago by Benilton Carvalho4.3k
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rma and brightness of exon arrays
... Hi, I am using rma to normalize a set of Affymetrix exon 1.0 ST arrays. I have done this both with the oligo package and with the Affymetrix Power Tools to get equivalent results. I find that the first principal component is completely determined by one of the quality measures, namely pos_control_ ...
oligo written 6.9 years ago by Rob Dunne230
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Comment: C: scan date information
... Thanks for that. I am not using the development version yet but I will look out for the new slot. Saroj, your method doesn't work for me, perhaps your cel file is ascii? strings SB_20D.CEL | grep DatHeader However, I have found $ grep --text d.a.t.e. SB_20D.CEL text/plainaffymetrix-scan-date(2008 ...
written 10.0 years ago by Rob Dunne230
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Comment: C: Continued problems with pdInfoBuilder
... Sean Davis wrote: > > > On Mon, Nov 17, 2008 at 7:00 PM, Harry Mangalam > > wrote: > > Like Rob Dunne previously, I'm trying to use pdInfoBuilder to generate > a pkg for the RaGene-1_0-st-v1 series, but am getting the same error > that he was finally able to re ...
written 10.8 years ago by Rob Dunne230
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Comment: C: inquiry for CDF file
... James W. MacDonald wrote: > Did you upgrade to R-devel, or simply install the devel version of > pdInfoBuilder in your R-2.6.2 installation? > Hi James, I just installed the devel version of pdInfoBuilder in my R-2.6.2 installation. I have now installed R-devel and pdInfoBuilder is worki ...
written 11.0 years ago by Rob Dunne230
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Answer: A: inquiry for CDF file
... Hi Benilton, yes, version 1.5.2 (and an upgrade of oligo and oligoClasses) fixed the problem. However the function "readPgfEnv" is not found Bye Rob library(pdInfoBuilder) pgfFile <- "RaGene-1_0-st-v1.r3.pgf" clfFile <- "RaGene-1_0-st-v1.r3.clf" transFile <- " RaGene-1_0-st-v1.na25.rn ...
written 11.0 years ago by Rob Dunne230

Latest awards to Rob Dunne

Popular Question 6.6 years ago, created a question with more than 1,000 views. For R matrix size limits and array data

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