Dear All, Taking HG-U133_PLUS_2 as an example, one probeset consists of 11 individual probes. I'd like to exclude few non-specific probes from one probeset for genes of interest before the subsequent all analysis. I searched the Archive. It seemed I need to generate a customized CDF file. I am just wondering whether there are some relatively simple methods. If not, could someone show how to modify the pre-existing HG- U133_PLUS_2 CDF file to exclude few probes? Many thanks ahead. Best regards, ------------------------------------------------------------- Yong Zhang Ph.D, Research Scholar Manyuan Long's Lab University of Chicago

03/03/2008 04:42 pkuonline scripsit > Dear All, > > Taking HG-U133_PLUS_2 as an example, one probeset consists of 11 individual probes. I'd like to exclude few non-specific probes from one probeset for genes of interest before the subsequent all analysis. I searched the Archive. It seemed I need to generate a customized CDF file. I am just wondering whether there are some relatively simple methods. If not, could someone show how to modify the pre-existing HG- U133_PLUS_2 CDF file to exclude few probes? > > Many thanks ahead. > > Best regards, > ------------------------------------------------------------- > Yong Zhang > Ph.D, Research Scholar > Manyuan Long's Lab > University of Chicago > Dear Yong suppose you want to remove the 4-th probe in probeset 1552391_at, then the code would be about as follows. You will need to do this after attaching the hgu133plus2cdf package and before calling functions like rma. > library("hgu133plus2cdf") > ls(hgu133plus2cdf)[100] [1] "1552391_at" > hgu133plus2cdf$"1552391_at" pm mm [1,] 618104 619268 [2,] 216159 217323 [3,] 353306 354470 [4,] 165282 166446 [5,] 658545 659709 [6,] 704429 705593 [7,] 867194 868358 [8,] 541423 542587 [9,] 932914 934078 [10,] 362488 363652 [11,] 1002956 1004120 > hgu133plus2cdf$"1552391_at" = hgu133plus2cdf$"1552391_at"[-4,] > hgu133plus2cdf$"1552391_at" pm mm [1,] 618104 619268 [2,] 216159 217323 [3,] 353306 354470 [4,] 658545 659709 [5,] 704429 705593 [6,] 867194 868358 [7,] 541423 542587 [8,] 932914 934078 [9,] 362488 363652 [10,] 1002956 1004120 > sessionInfo() R version 2.7.0 Under development (unstable) (2008-03-02 r44660) x86_64-unknown-linux-gnu locale: LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT .UTF-8;LC_MONETARY=it_IT.UTF-8;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133plus2cdf_2.0.0 fortunes_1.3-4 loaded via a namespace (and not attached): [1] tools_2.7.0 -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber

See http://article.gmane.org/gmane.science.biology.informatics.conduct or/9869/ Jenny At 10:42 PM 3/2/2008, pkuonline wrote: >Dear All, > >Taking HG-U133_PLUS_2 as an example, one probeset consists of 11 >individual probes. I'd like to exclude few non-specific probes from >one probeset for genes of interest before the subsequent all >analysis. I searched the Archive. It seemed I need to generate a >customized CDF file. I am just wondering whether there are some >relatively simple methods. If not, could someone show how to modify >the pre-existing HG-U133_PLUS_2 CDF file to exclude few probes? > >Many thanks ahead. > >Best regards, >------------------------------------------------------------- >Yong Zhang >Ph.D, Research Scholar >Manyuan Long's Lab >University of Chicago > >_______________________________________________ >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu