Hello, I've been using Bioconductor to do the background correction and normalization of my data, but I want to use the probe values themselves instead of a summary value for my statistical analyses. I am able to export the matrix of pm values, but the first column lists the AffyID and probe number together (e.g., 100_g_at1, 100_g_at2, 100_g_at3, etc.). Is there an easy way to separate these? I need two columns: one with just the AffyID (100_g_at) and one with the probe number (1, 2, 3, etc.). I don't need these two columns in the pm matrix I export, because I can combine the two in SAS. Thanks in advance, Jenny Jenny Drnevich, Ph.D. Department of Animal Biology 515 Morrill Hall 505 S Goodwin Ave Urbana, IL 61801 USA ph: 217-244-6826 fax: 217-244-4565 e-mail: drnevich@uiuc.edu

I am not sure I get the whole, but I getting "ProbeSet" objects might be want you want (method 'probeset' for 'AffyBatch'). Hopin' it helps, L. On Tue, Jul 15, 2003 at 11:15:30AM -0500, Jenny Drnevich wrote: > Hello, > > I've been using Bioconductor to do the background correction and > normalization of my data, but I want to use the probe values themselves > instead of a summary value for my statistical analyses. I am able to export > the matrix of pm values, but the first column lists the AffyID and probe > number together (e.g., 100_g_at1, 100_g_at2, 100_g_at3, etc.). Is there an > easy way to separate these? I need two columns: one with just the AffyID > (100_g_at) and one with the probe number (1, 2, 3, etc.). I don't need > these two columns in the pm matrix I export, because I can combine the two > in SAS. > > Thanks in advance, > Jenny > > Jenny Drnevich, Ph.D. > Department of Animal Biology > 515 Morrill Hall > 505 S Goodwin Ave > Urbana, IL 61801 > USA > > ph: 217-244-6826 > fax: 217-244-4565 > e-mail: drnevich@uiuc.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent

the probeNames method gives you the probeNames in the same ordering as the pm method (if you use the default cdfenvironments). within a probe set the pms are ordered by probe number (position along the transcript). probeNames has an "mm" argument that if made TRUE does the same for the MM probes. example: library(affydata) data(Dilution) pms <- pm(Dilution) pmnames <- probeNames(Dilution) you dont have to save the numbers because they are already ordered. for exmaple, for probe "1001_at", you can see a table of the values you want by doing the equivelant in SAS to: Index <- which(pmnames=="1001_at") data.frame(pm=pms[Index],names=pmnames[Index],number=seq(along=Index)) Tue, 15 Jul 2003, Jenny Drnevich wrote: > Hello, > > I've been using Bioconductor to do the background correction and > normalization of my data, but I want to use the probe values themselves > instead of a summary value for my statistical analyses. I am able to export > the matrix of pm values, but the first column lists the AffyID and probe > number together (e.g., 100_g_at1, 100_g_at2, 100_g_at3, etc.). Is there an > easy way to separate these? I need two columns: one with just the AffyID > (100_g_at) and one with the probe number (1, 2, 3, etc.). I don't need > these two columns in the pm matrix I export, because I can combine the two > in SAS. > > Thanks in advance, > Jenny > > Jenny Drnevich, Ph.D. > Department of Animal Biology > 515 Morrill Hall > 505 S Goodwin Ave > Urbana, IL 61801 > USA > > ph: 217-244-6826 > fax: 217-244-4565 > e-mail: drnevich@uiuc.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Another lternative is to use base package functions using regular expressions and substring to break the AffyID information up into the two vectors.e .g. library(affydata) data(Dilution) pms <- pm(Dilution) AffyInfo <- dimnames(pms)[[1]] cutpos <- regexpr("\\d+$",AffyInfo, perl=T) # Under help(regexpr) #`perl=TRUE' will only be available if R was compiled against # PCRE: this is detected at configure time. All Unix and Windows # system should have it. AffyID <- substr(AffyInfo, 1, cutpos-1) probe <- as.numeric(substr(AffyInfo,cutpos, nchar(AffyInfo))) cbind(AffyInfo, AffyID,probe)[1:20,] marcus >>> Jenny Drnevich <drnevich@uiuc.edu> 16/07/2003 4:15:30 AM >>> Hello, I've been using Bioconductor to do the background correction and normalization of my data, but I want to use the probe values themselves instead of a summary value for my statistical analyses. I am able to exportt he matrix of pm values, but the first column lists the AffyID and probe number together (e.g., 100_g_at1, 100_g_at2, 100_g_at3, etc.). Is there ane asy way to separate these? I need two columns: one with just the AffyID (100_g_at) and one with the probe number (1, 2, 3, etc.). I don't need these two columns in the pm matrix I export, because I can combine the twoi n SAS. Thanks in advance, Jenny Jenny Drnevich, Ph.D. Department of Animal Biology 515 Morrill Hall 505 S Goodwin Ave Urbana, IL 61801 USA ph: 217-244-6826 fax: 217-244-4565 e-mail: drnevich@uiuc.edu _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidential to the named recipient and are not to be used by any other person and/or organisation. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail.