On 01/25/12 21:12, Valerie Obenchain wrote: > Hi Rocky, > > gsub() "finds and replaces". In this example we replace the dot with > an underscore. The double backslash in front of the dot is "escaping" > the dot because it is a special character (metacharacter). See ?regex > and ?gsub for details. > > gsub("\\.", "A", c("foo.bar", ".foo")) sorry, changed my example ... this should have been gsub("\\.", "_", c("foo.bar", ".foo")) > > In the line you have below there are two gsub() statements. We can > rewrite the statement in pieces, > > p <- phenoData(gse[[1]])$"characteristics_ch1" > x <- gsub("subtype: ", "", p) > subtype <- gsub("\\.", "_", x) > > Take a look at the output of each of these steps to better understand > what is going on. > > I don't understand the second part of your question, re: GSE11024. > What have you tried? Are you getting an error? > > > Valerie > > > > > > > On 01/24/12 23:01, haojam wrote: >> Bioconductor Group, >> >> >> >> Hi, >> >> I have a special request regarding PGSEA Package to identify >> downregulated >> genes. I am not clear about this line >> subtype<- gsub("\\.", "_",gsub("subtype: ", "", >> phenoData(gse[[1]])$"characteristics_ch1")) >> >> What does gsub ( ) mean for and \\ . I would like to look for GSE11024 >> having 5 subtypes and 0ne normal group, how could I proceed. >> >> >> >> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11024 >> GSM278765 - GSM278774 (10 samples) -> CC_KIDNEY >> GSM278775 - GSM278780 (6 samples) -> CHR_KIDNEY >> GSM278781 - GSM278792 (12 samples) -> NOR_KIDNEY >> GSM278793 - GSM278799 (7 samples) -> ON_KIDNEY >> GSM278800 - GSM278816 (17 samples) -> Pappilary_KIDNEY >> GSM278817 - GSM278843 (27 samples) -> WM_KIDNEY >> >> >> >> Warm regards, >> >> Rocky >> >> SNU College of Medicine >> >> Korea >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor