Just a quick guess here, but the .CDF file may go 3' to 5' while the probe package has this the standard way 5' to 3'. Biocondcutor is the correct place to post these issues. Good luck. ------ Justin Borevitz http://naturalvariation.org >-----Original Message----- >From: Hrishikesh Deshmukh [mailto:d_hrishikesh@yahoo.com] >Sent: Wednesday, February 09, 2005 9:53 AM >To: Justin Borevitz >Subject: Sequence data and filtering results > >Hello Dr.Borevitz, > >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 > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com