I have made some progress. Change dir(to where CEL files are saved) Data <- ReadAffy() eset <- rma(Data) my.pm.data <- pm(Data) write.table (my.pm.data, file = "pmprobes3.csv", sep = ",", col.names = TRUE, row.names = probeNames(Data)) This results in the following: Probe Sam1 Sam2 Sam3 Sam4 1415670_at01 340 383 376 320 1415670_at02 794 932 734 697 1415670_at03 1117 1366 1013 932 1415670_at04 97 97 148 94 1415670_at05 387 405 367 402 1415670_at06 485 553 391 343 1415670_at07 458 509 410 385 1415670_at08 507 684 616 545 1415670_at09 311 392 576 463 1415670_at10 691 822 688 588 1415670_at11 512 726 3201 2317 1415671_at01 1230 1212 873 770 1415671_at02 886 877 794 729 1415671_at03 1472 1682 1263 1152 1415671_at04 1171 1214 948 914 1415671_at05 390 479 435 396 1415671_at06 462 513 423 389 1415671_at07 987 1151 1102 815 1415671_at08 992 1066 1203 1013 1415671_at09 489 534 501 385 1415671_at10 401 509 379 293 1415671_at11 1443 1686 1410 1215 How can I get the p-value for each probe? >===== Original Message From Frank Duan <fhduan@gmail.com> ===== >use PM function in Affy package. > >Frank > > >On Mon, 4 Oct 2004 16:48:12 -0400, kvyas <kvyas@utk.edu> wrote: >> I have CEL files from Affymetrix Mouse Array 430_2 and am trying to get the >> the individual PM intensities (11 per gene) for each sample. I would like to >> write out this into a tab delimited text file. Where am I stalling? This is >> what I've done: >> >> Change dir(to where CEL files are saved) >> Data <- ReadAffy() >> eset <- rma(Data) >> write.exprs(eset, file="mydata.txt") >> >> With this I am only able to get the average intensities per gene not the >> intensity per probe of each gene. >> >> Please help me out. >> >> Kanan >> >> ______________________________________________ >> R-help@stat.math.ethz.ch mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >> ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting- guide.html