Dear Jim, Thank you for pointing John to the correct library-files, however I just realized that you mention the design-time annotation files, which are outdated. People should always download the "NetAffx Annotation Files" which contain the latest annotations (currently Release 30). Best regards Christian On 6/15/10 3:10 PM, James W. MacDonald wrote: > > > John Coulthard wrote: >> Dear list >> >> I've got 6x2 Human Exon 1.0 ST arrays to analyse and 3gB of ram so I >> believe I need to use xps. >> The xps vignette, appendix A.1. says... >> "we need to create ROOT scheme fi les directly from the A ymetrix >> source files, which need to be downloaded >> first from the A ymetrix web site." >> >> I think the web page I need to download from is... >> http://www.affymetrix.com/browse/products.jsp?productId=131452&navM ode=34000&navAction=jump&aId=productsNav#1_3 >> >> >> but there is no file that ends with ?annot.csv?. Should I rename one >> of the other annotation files? Which one? > > How about the one labeled 'HuEx-1_0-st-v2 Annotations, Probeset, > Hg18/Build36, CSV (43 MB 10/06/06)', under 'Design Time Annotation Files'? > >> >> The CDF file on this page says 'unsupported' so maybe I should be >> looking for CLF-, PGF-fi les, but they're not on this page either. > > Yes they are, under the link 'Human Exon 1.0 ST Array Analysis (zip, 131 > MB)'. > > Best, > > Jim > > >> >> Can anyone help me out with what to download from where? >> >> Thanks >> John >> >> >> _________________________________________________________________ >> Hotmail: Powerful Free email with security by Microsoft. >> >> [[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 >

Hi Benilton, i'm using oligo in a processing pipeline which runs out of RAM with >15 exon arrays, so I was considering switching to xps. However, i'm intrigued by your comment re 'if you think you have enough RAM for the expression matrix'. Are you implying that you can use oligo on quite large numbers of exon arrays & that it's only when you create the expression object that you'll run out of RAM? cheers, Mark ----------------------------------------------------- Mark Cowley, PhD Peter Wills Bioinformatics Centre Garvan Institute of Medical Research, Sydney, Australia ----------------------------------------------------- On 15/06/2010, at 9:11 PM, Benilton Carvalho wrote: > Dear John, > > Indeed, xps is one solution. If you're willing to try another > approach, you can also use the oligo package. It's experimental, as > described in one of the vignettes, but the following should get you > going: > > library(oligo) > ## enable large dataset management > library(ff) > ## set a place for temp files > ## otherwise it'll use the current dir > ldPath("/path/to/temp") > cels = list.celfiles() > raw = read.celfiles(cels) > core = rma(raw, target="core") > exprsCore = exprs(core) > ## save in a tab-delim file > write.table.ffdf(as.ffdf(exprsCore), file="core.txt", sep="\t", quote=FALSE) > ## if you think you have enough RAM for the expression matrix > expression = exprsCore[] > > In case you observe anything unexpected, let me know. > > b > > On 15 June 2010 11:43, John Coulthard <bahhab at="" hotmail.com=""> wrote: >> >> Dear list >> >> I've got 6x2 Human Exon 1.0 ST arrays to analyse and 3gB of ram so I believe I need to use xps. >> The xps vignette, appendix A.1. says... >> "we need to create ROOT scheme fi les directly from the A ymetrix source files, which need to be downloaded >> first from the A ymetrix web site." >> >> I think the web page I need to download from is... >> http://www.affymetrix.com/browse/products.jsp?productId=131452&navM ode=34000&navAction=jump&aId=productsNav#1_3 >> >> but there is no file that ends with ?annot.csv?. Should I rename one of the other annotation files? Which one? >> >> The CDF file on this page says 'unsupported' so maybe I should be looking for CLF-, PGF-fi les, but they're not on this page either. >> >> Can anyone help me out with what to download from where? >> >> Thanks >> John >> >> >> >> _________________________________________________________________ >> Hotmail: Powerful Free email with security by Microsoft. >> >> [[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 >> > > _______________________________________________ > 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