Dear Bioconductorians, I have written a script which reads in Affymetrix data, filters based on intensity values and then pulls sequence data for the probes which satisfy the intensity based filter. I notice that results given by the script are different from the sequence data files which Affymetrix supplies! Here are top three seq. from my result and below these are the sequences for the same probe ID's from Affymetrix seq file, why do i different sequences, i am attaching the script file for your perusal, your help is appreciated. h.pbn my.in.seq 1000_at TTGCGCTACAGCTAGGCCGCATGCT 1000_at TGGAAGCCAGGAAGGCCTATGTGAA 100_g_at TTCCCTGAAGGAACATTCCTTAGTC >probe:HG-U95Av2:1000_at:399:559; TCTCCTTTGCTGAGGCCTCCAGCTT >probe:HG-U95Av2:1000_at:544:185; AGGCCTCCAGCTTCAGGCAGGCCAA >probe:HG-U95Av2:1000_at:530:505; CCAGCTTCAGGCAGGCCAAGGCCTT >probe:HG-U95Av2:1000_at:617:349; AGCTCAGGTGGCCCCAGTTCAATCT >probe:HG-U95Av2:1000_at:459:489; AGTTCTGGAATGGAAGGGTTCTGGC >probe:HG-U95Av2:1000_at:408:545; TAGGGACTCAGGGCCATGCCTGCCC >probe:HG-U95Av2:1000_at:484:311; TTCCCTGAAGGAACATTCCTTAGTC >probe:HG-U95Av2:1000_at:548:333; GAAGGAACATTCCTTAGTCTCAAGG >probe:HG-U95Av2:1000_at:578:369; CTTAGTCTCAAGGGCTAGCATCCCT >probe:HG-U95Av2:1000_at:498:465; CTCAAGGGCTAGCATCCCTGAGGAG >probe:HG-U95Av2:1000_at:503:441; GGCTAGCATCCCTGAGGAGCCAGGC >probe:HG-U95Av2:1000_at:482:439; CTGTCAAAGCTGTCACTTCGCGTGC >probe:HG-U95Av2:1000_at:397:545; AAGCTGTCACTTCGCGTGCCCTCGC >probe:HG-U95Av2:1000_at:352:465; CGCGTGCCCTCGCTGCTTCTGTGTG >probe:HG-U95Av2:1000_at:253:495; CCCTCGCTGCTTCTGTGTGTGGTGA >probe:HG-U95Av2:1000_at:228:631; CTGCTTCTGTGTGTGGTGAGCAGAA ++++++++++++++++++++++++++++++++++++++++ >probe:HG-U95Av2:100_g_at:497:273; CATCTGGAACAGCTGCTCTTGGTCA >probe:HG-U95Av2:100_g_at:208:557; AACAGCTGCTCTTGGTCACCCATCT >probe:HG-U95Av2:100_g_at:495:355; GCTGCTCTTGGTCACCCATCTTGAC >probe:HG-U95Av2:100_g_at:478:371; TTGAGGTGCTGCAGGCCAGTGATAA >probe:HG-U95Av2:100_g_at:612:429; CTACCCCGGCTGCAGGAGCTGCTAC >probe:HG-U95Av2:100_g_at:563:317; GCAGGAGCTGCTACTGTGCAACAAC >probe:HG-U95Av2:100_g_at:223:559; GCAGCCTGCAGTGCTCCAGCCTCTT >probe:HG-U95Av2:100_g_at:523:575; GTCCTCCTCAACCTGCAGGGTAACC >probe:HG-U95Av2:100_g_at:551:445; AGGGTAACCCGCTGTGCCAAGCGGT >probe:HG-U95Av2:100_g_at:509:475; GCATCTTGGAGCAACTGGCTGAACT >probe:HG-U95Av2:100_g_at:576:249; AGCAACTGGCTGAACTGCTGCCTTC >probe:HG-U95Av2:100_g_at:568:349; CTGGCTGAACTGCTGCCTTCAGTTA >probe:HG-U95Av2:100_g_at:523:441; GCTGCCTTCAGTTAGCAGCGTCCTC >probe:HG-U95Av2:100_g_at:562:421; CCTTCAGTTAGCAGCGTCCTCACCT >probe:HG-U95Av2:100_g_at:622:473; AGTTAGCAGCGTCCTCACCTAAGAG >probe:HG-U95Av2:100_g_at:567:607; GCCCTTTAACTTATTGGGACTGAAT library(affy) library(hgu95av2probe) data(hgu95av2probe) summary(hgu95av2probe) Data <- ReadAffy() pmi <- pm(Data) mmi <- mm(Data) pbn <- probeNames(Data) rng.pmi <- apply(pmi,1,range) rng.mmi <- apply(mmi,1,range) in.boundspm <- ((rng.pmi[1,] >=200) & (rng.pmi[1,] <=20000)) in.boundsmm <- ((rng.mmi[1,] >=200) & (rng.mmi[1,] <=20000)) in.bounds <- (in.boundspm & in.boundsmm) length(pmi[,1]) ac1 <- 1:201800 ac2 <- ac1[in.bounds] h.pbn <- pbn[ac2] h.pmi <- pmi[ac2,] h.mmi <- mmi[ac2,] my.in.seqpm <- hgu95av2probe$sequence[in.boundspm] my.in.seqmm <- hgu95av2probe$sequence[in.boundsmm] my.in.seq <- hgu95av2probe$sequence[in.bounds] seq.data<- cbind(h.pbn,my.in.seq) write.table(seq.data, file="SeqData.txt",quote =F,row.names=F,col.names=T,sep = " ") Eagerly waiting for your reply. Thanks in advance. Hrishi