Hi Christian, Thanks very much indeed. I can confirm that xps 1.2.6 certainly works as advertised, and produces output comparable with what I've been getting with APT. I'll let you know if I encounter any problems, but so far I've not found any! Cheers, Tim 2009/2/24 cstrato <cstrato at="" aon.at="">: > Dear Tim, > > I am glad to inform you that a new version of xps is now available from BioC > (xps_1.2.6 and xps_1.3.6), and I would very ?much appreciate if you could > test the new version. > > Please note that release 4 (r4) of the HuGene array converts it to an exon > array, so you need to create the scheme as follows: > > xps.scheme <- > import.exon.scheme("Scheme_HuGene10stv1r4_na27_2",filedir=scmdir, > > layoutfile=paste(libdir,"HuGene-1_0-st-v1.r4.analysis-lib-files /HuGene-1_0-st-v1.r4.clf",sep="/"), > > schemefile=paste(libdir,"HuGene-1_0-st-v1.r4.analysis-lib-files /HuGene-1_0-st-v1.r4.pgf",sep="/"), > > probeset=paste(anndir,"Version09Feb/HuGene- 1_0-st-v1.na27.2.hg18.probeset.csv",sep="/"), > > transcript=paste(anndir,"Version09Feb/HuGene- 1_0-st-v1.na27.hg18.transcript.csv",sep="/")) > > > If you summarize the data on the transcript level you should get identical > results as before: > > xps.rma <- rma(xps.cel, "HuGeneMixRMAcore", background="antigenomic", > ? ? ? ? ? ? ?option="transcript", exonlevel="core+affx") > > > In addition, you can now summarize the data on the probeset (exon) level: > > xps.rma.ps <- rma(xps.cel, "HuGeneMixRMAcorePS", background="antigenomic", > ? ? ? ? ? ? ? ? option="probeset", exonlevel="core+affx") > > > Please let me know if the new version works as expected. > > Best regards > Christian > > > Tim Rayner wrote: >> >> Dear Christian, >> >> Thank you very much for your help - reverting to the older r3 files >> does indeed solve the problem. I'll look forward to hearing about the >> new version of the xps package, and I'd be more than happy to help >> test it if needed. >> >> Best regards, >> >> Tim >> >> 2009/2/17 cstrato <cstrato at="" aon.at="">: >> >>> >>> Dear Tim, >>> >>> First, I am glad to hear that my package works on 64-bit OS w/o problems. >>> >>> Luckily, the solution to your problem is simple. Please use the following >>> pgf and clf files in your code to create xps.scheme: >>> - HuGene-1_0-st-v1.r3.clf >>> - HuGene-1_0-st-v1.r3.pgf >>> >>> The reason is as follows: >>> About two weeks ago Affymetrix has updated the pgf file to allow >>> customers >>> to use HuGene as a cheaper exon array. For this purpose, they have >>> created >>> an additional "HuGene-1_0-st-v1.na27.hg18.probeset.csv" file and have >>> changed the probesets in the *.pgf file. Instead of >>> "transcript_cluster_id" >>> the probes are now mapped to "probeset_id" of the new probeset annotation >>> file. For this reason xps recognizes only the 57 affx-controls when >>> parsing >>> the *.pgf file, and thus only these 57 controls will be summarized. >>> >>> I am currently in the process to update my package to allow using HuGene >>> arrays as exon arrays, and I will inform you once I have uploaded the new >>> version. Until then I must ask you to use the older *.r3.pgf file. >>> >>> Best regards >>> Christian >>> _._._._._._._._._._._._._._._._._._ >>> C.h.r.i.s.t.i.a.n ? S.t.r.a.t.o.w.a >>> V.i.e.n.n.a ? ? ? ? ? A.u.s.t.r.i.a >>> e.m.a.i.l: ? ? ? ?cstrato at aon.at >>> _._._._._._._._._._._._._._._._._._ >>> >>> >>> Tim Rayner wrote: >>> >>>> >>>> Hi, >>>> >>>> I'm seeing what appears to be odd behaviour from the xps rma() method >>>> when trying to summarize a small test dataset from the >>>> HuGene-1_0-st-v1 array. The oddness is that whatever options I pass to >>>> rma(), I only ever get summary data for 57 probe sets back (obviously >>>> I'd expect rather more than that). >>>> >>>> I'm using 64-bit Mac OSX, and I believe I've installed everything >>>> correctly and imported the probe annotation from the latest chip >>>> library files on Affy's web site. I did have to compile ROOT from >>>> source to support the 64-bit architecture, but that went pretty >>>> smoothly. After some hours of poking through the xps code I'm a little >>>> suspicious about the probe masking, but not much wiser, I'm afraid. >>>> >>>> I should just briefly mention that I can run rma over the same data >>>> set by using the oligo package, so I think the data files are fine. >>>> >>>> Attached is a sample session, which I've just run from scratch to >>>> confirm the problem, and my sessionInfo. I'm wondering if anyone else >>>> has seen this, or if I've just made some fundamental error. >>>> >>>> Many thanks, >>>> >>>> Tim Rayner >>>> >>>> >>>> >>>> ############################################# >>>> ## sessionInfo(): >>>> >>>> >>>> >>>>> >>>>> sessionInfo() >>>>> >>>>> >>>> >>>> R version 2.8.1 Patched (2009-01-19 r47650) >>>> i386-apple-darwin9.6.0 >>>> >>>> locale: >>>> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 >>>> >>>> attached base packages: >>>> [1] tools ? ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] Biobase_2.2.2 xps_1.2.5 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] tcltk_2.8.1 >>>> >>>> >>>> >>>> ############################################## >>>> ## Session commands: >>>> library('xps') >>>> celdir=getwd() >>>> celfiles=list.files(pattern='.*.CEL') >>>> libdir <- '/Users/tfr23/Documents/resources/HuGene-1_0/' >>>> xps.scheme <- import.genome.scheme(filename='HuGene- 1_0-st-v1-r4', >>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?filedir=libdir, >>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?layoutfile=paste(libdir, >>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?'HuGene-1_0-st-v1.r4.clf', >>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?sep=''), >>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?schemefile=paste(libdir, >>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?'HuGene-1_0-st-v1.r4.pgf', >>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?sep=''), >>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?transcript=paste(libdir, >>>> >>>> 'HuGene-1_0-st-v1.na27.hg18.transcript.csv', >>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?sep=''), >>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?verbose=TRUE) >>>> >>>> xps.cel<-import.data(xps.scheme, 'HuGeneCelData', celdir=celdir, >>>> celfiles=celfiles) >>>> >>>> xps.cel<-attachInten(xps.cel) >>>> >>>> xps.rma <- rma(xps.cel, >>>> ? ? ? ? ? ? ?filename='HuGeneMixRMAMetacore', >>>> ? ? ? ? ? ? ?exonlevel='metacore+affx', >>>> ? ? ? ? ? ? ?background='antigenomic', >>>> ? ? ? ? ? ? ?normalize=TRUE) >>>> >>>> ###################################### >>>> ## Session output: >>>> >>>> Welcome to xps version 1.2.5 >>>> ? an R wrapper for XPS - eXpression Profiling System >>>> ? (c) Copyright 2001-2009 by Christian Stratowa >>>> >>>> Creating new file >>>> >>>> </users>... >>>> Importing >>>> </users> >>>> as <hugene-1_0-st-v1.cxy>... >>>> ?<1102500> records imported...Finished >>>> New dataset <hugene-1_0-st-v1> is added to Content... >>>> Importing >>>> >>>> </users> >>>> as <hugene-1_0-st-v1.ann>... >>>> ?Number of transcripts is <33297>. >>>> ?<33297> records read...Finished >>>> ?<33297> records imported...Finished >>>> Importing >>>> </users> >>>> as <hugene-1_0-st-v1.scm>... >>>> ?Reading data from input file... >>>> ?Number of probesets is <257430>. >>>> Note: Number of annotated probesets <33297> is not equal to number of >>>> probesets <257430>. >>>> ?<257430> records read...Finished >>>> ?Sorting data for probeset_type and position... >>>> ?Total number of controls is <4371> >>>> ?Note: no data for probeset type: control->chip... >>>> ?Filling trees with data for probeset type: normgene, rescue... >>>> ?Filling trees with data for probeset type: control->bgp... >>>> ?Filling trees with data for probeset type: control->affx... >>>> ?<33252> probeset tree entries read...Finished >>>> ?Number of control->affx probesets is <57>. >>>> ?Filling trees with data for probeset type: main... >>>> ?Filling trees with data for non-annotated probesets... >>>> ?<861493> records imported...Finished >>>> ?<257430> total transcript units imported. >>>> ?Genome cell statistics: >>>> ? ? Number of unit cells: minimum = 1, ?maximum = 1189 >>>> Opening file >>>> </users> >>>> in <read> mode... >>>> Creating new file >>>> </users>... >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 020206a="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 1 cells with minimal intensity 23 >>>> ? ? 1 cells with maximal intensity 35735 >>>> New dataset <dataset> is added to Content... >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 020305="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 2 cells with minimal intensity 20 >>>> ? ? 1 cells with maximal intensity 24768 >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 030804="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 6 cells with minimal intensity 25 >>>> ? ? 1 cells with maximal intensity 38526 >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 040107="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 2 cells with minimal intensity 22 >>>> ? ? 1 cells with maximal intensity 20150 >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 061004="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 2 cells with minimal intensity 20 >>>> ? ? 1 cells with maximal intensity 21650 >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 070205="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 2 cells with minimal intensity 21 >>>> ? ? 1 cells with maximal intensity 23005 >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 090305="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 22 cells with minimal intensity 21 >>>> ? ? 1 cells with maximal intensity 21205 >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 110806b="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 1 cells with minimal intensity 21 >>>> ? ? 1 cells with maximal intensity 22958 >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 150107="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 2 cells with minimal intensity 19 >>>> ? ? 1 cells with maximal intensity 23606 >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 150405="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 4 cells with minimal intensity 24 >>>> ? ? 1 cells with maximal intensity 24268 >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 190706="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 6 cells with minimal intensity 21 >>>> ? ? 1 cells with maximal intensity 22769 >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -="" 300605="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 2 cells with minimal intensity 20 >>>> ? ? 1 cells with maximal intensity 22309 >>>> Importing </users>>>> 090213.CEL> as <affy 0104="" -040205="" cd8="" -="" 090213.cel="">... >>>> ?hybridization statistics: >>>> ? ? 1 cells with minimal intensity 23 >>>> ? ? 1 cells with maximal intensity 22497 >>>> Creating new file >>>> </users>... >>>> Opening file >>>> </users> >>>> in <read> mode... >>>> Preprocessing data using method <preprocess>... >>>> ?Background correcting raw data... >>>> ? ? setting selector mask for typepm <8252> >>>> ? ? calculating background for <affy 0104="" -="" 020206a="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?1378 cells with maximal intensity 151.284 >>>> ? ? calculating background for <affy 0104="" -="" 020305="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?2 cells with maximal intensity 75.9992 >>>> ? ? calculating background for <affy 0104="" -="" 030804="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?28 cells with maximal intensity 122.454 >>>> ? ? calculating background for <affy 0104="" -="" 040107="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?13 cells with maximal intensity 154.02 >>>> ? ? calculating background for <affy 0104="" -="" 061004="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?47 cells with maximal intensity 101.165 >>>> ? ? calculating background for <affy 0104="" -="" 070205="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?25 cells with maximal intensity 94.408 >>>> ? ? calculating background for <affy 0104="" -="" 090305="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?220 cells with maximal intensity 52.9483 >>>> ? ? calculating background for <affy 0104="" -="" 110806b="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?97 cells with maximal intensity 136.739 >>>> ? ? calculating background for <affy 0104="" -="" 150107="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?1055 cells with maximal intensity 105.265 >>>> ? ? calculating background for <affy 0104="" -="" 150405="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?36 cells with maximal intensity 128.385 >>>> ? ? calculating background for <affy 0104="" -="" 190706="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?957 cells with maximal intensity 135.396 >>>> ? ? calculating background for <affy 0104="" -="" 300605="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?865 cells with maximal intensity 49.4309 >>>> ? ? calculating background for <affy 0104="" -040205="" cd8="" -="" 090213.cel="">... >>>> ? ? background statistics: >>>> ? ? ? ?1097995 cells with minimal intensity 0 >>>> ? ? ? ?650 cells with maximal intensity 140.053 >>>> ?Normalizing raw data... >>>> ? ? normalizing data using method <quantile>... >>>> ? ? setting selector mask for typepm <8252> >>>> ? ? ? ?finished filling <13> arrays. ? ? ? ? ? 90213>... >>>> ? ? ? ?finished filling <13> trees. ? ? ? ? ?090213.cqu>... >>>> ?Converting raw data to expression levels... >>>> ? ? summarizing with <medianpolish>... >>>> ? ? setting selector mask for typepm <8252> >>>> ? ? setting selector mask for typepm <8252> >>>> ? ? calculating expression for <57> of <257430> units...Finished. >>>> ? ? expression statistics: >>>> ? ? ? ?minimal expression level is <19.8498> >>>> ? ? ? ?maximal expression level is <8953.24> >>>> ?preprocessing finished. >>>> Opening file >>>> </users> >>>> in <read> mode... >>>> Opening file </users> >>>> in <read> mode... >>>> Exporting data from tree <*> to file >>>> </users>... >>>> Reading entries from <hugene-1_0-st-v1.ann> ...Finished >>>> <57> of <57> records exported. >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>>> >>>> >>> >>> >> >> >> > >