[BioC] RE: Sequence data and filtering results

[Justin Borevitz]

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 at 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
>
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