Hi Mark and Hervé, Thanks a lot. I will try that. I was using strsplit(x,"|"), without the backslashes. Thanks again. Sincerely, Hari 2009/6/16 Hervé Pagès <hpages@fhcrc.org> > Hi Hari, Mark, > > Mark Robinson wrote: > >> Hi Hari. >> >> strsplit() will work, its just sensitive. For starters, you might try: >> >> > x <- c("ref|NM_004564|ref|PET112L:2131|mgc|BC130348:2158", >> + "ref|NM_007266|ref|XAB1:2255|mgc|BC007451:2239","mgc|BC034752:79") >> > >> > strsplit(x,"\\|") >> [[1]] >> [1] "ref" "NM_004564" "ref" "PET112L:2131" >> [5] "mgc" "BC130348:2158" >> >> [[2]] >> [1] "ref" "NM_007266" "ref" "XAB1:2255" >> [5] "mgc" "BC007451:2239" >> >> [[3]] >> [1] "mgc" "BC034752:79" >> > > Note that it's better here to use strsplit() with fixed=TRUE. Then no > need to escape the | and in addition strsplit() will be much faster... > > Cheers, > H. > > > >> >> And, for extracting the first 2 columns, maybe you'll want to migrate >> towards something like: >> >> > t(sapply(x, FUN=function(u) strsplit(u, "\\|")[[1]][1:2], >> USE.NAMES=FALSE)) >> [,1] [,2] >> [1,] "ref" "NM_004564" >> [2,] "ref" "NM_007266" >> [3,] "mgc" "BC034752:79" >> >> Hope that gets you started. >> >> Cheers, >> Mark >> >> >> On 17/06/2009, at 7:54 AM, Hari Easwaran wrote: >> >> Hi all, >>> I am working with Agilent microarray data and trying to extract only the >>> accession numbers from the output probe annotation. Basically I have a >>> column detailing the probe as follows: >>> >>> ref|NM_004564|ref|PET112L:2131|mgc|BC130348:2158 >>> ref|NM_007266|ref|XAB1:2255|mgc|BC007451:2239 >>> mgc|BC034752:79 >>> ref|NM_057094|ref|CRYBA2:-2513|ref|NM_005209:-2519|ref|NM_194302:4 5605|mirna|hsa-mir-375:5790 >>> >>> ... >>> >>> I am trying to extract only the Refseq IDs (in this case NM_004564, >>> NM_007266, NM_057094, NM_005209, NM_194302.....) and create a new column >>> with the IDs. I am not able to figure out how to do this. I tried using >>> the >>> function 'strsplit', but it doesn't work. >>> I am a newbie to R/Bioconductor and would appreciate if someone can help. >>> >>> Thanks. >>> Hari >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> ------------------------------ >> Mark Robinson, PhD (Melb) >> Epigenetics Laboratory, Garvan >> Bioinformatics Division, WEHI >> e: m.robinson@garvan.org.au >> e: mrobinson@wehi.edu.au >> p: +61 (0)3 9345 2628 >> f: +61 (0)3 9347 0852 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]