my bad. Because i2xy is not exposed, you need to do sth like: idx = oligo:::i2xy(pmi, data_bpmap) B On Nov 15, 2007, at 9:36 PM, "Gayla Olbricht" <ghobbs at="" stat.purdue.edu=""> wrote: > Hi Benilton, > > Thanks for the advice. > > So, when I ran the first thing you suggested, I got the following > error: > >> xy.coord <- getPD(data_bpmap) [pmindex(data_bpmap), c("X", "Y")] > Error in getPD(data_bpmap)[pmindex(data_bpmap), c("X", "Y")] : > object is not subsettable > > But, was able to use your suggestion as a hint to get at the X,Y > coordinates for PM values by the following: > feature<-getPD(data_bpmap) > PMxcoord<-feature$X[pmindex(data_bpmap)] > PMycoord<-feature$Y[pmindex(data_bpmap)] > > This seems to give me what I need. > > I'm still not exactly sure how the pmindex is calculated, but maybe > the x,y coordinate information will be all I need. > > I did try running the function i2xy and got the following: > >> pmi <- pmindex(data_bpmap) >> xy.coord2 <- i2xy(pmi, data_bpmap) > Error: could not find function "i2xy" > > The same thing happened when I tried "indices2xy" instead. > > I would still be interested to know if the i2xy function can work, > but I guess I can do without it since I have the x,y information. > > Thanks again for your quick response and help with this! > -Gayla > > > > > > > > ----- Original Message ----- From: "Benilton Carvalho" <bcarvalh at="" jhsph.edu=""> > > To: "Gayla Olbricht" <ghobbs at="" stat.purdue.edu=""> > Cc: <bioconductor at="" stat.math.ethz.ch=""> > Sent: Thursday, November 15, 2007 3:56 PM > Subject: Re: [BioC] pmindex in oligo package > > >> say "TilingFeatureSetObject" is your object, you should be able to >> get X and Y coordinates by: >> >> xy.coord <- getPD(TilingFeatureSetObject) [pmindex >> (TilingFeatureSetObject), c("X", "Y")] >> >> i can't check right now, sorry, but i think there's an (unexposed) >> function that should help you with that: >> >> pmi <- pmindex(TilingFeatureSet) >> xy.coord2 <- i2xy(pmi, TilingFeatureSet) >> >> let us know how these go and i'll get back to you ASAP. >> >> b >> >> On Nov 15, 2007, at 3:43 PM, Gayla Olbricht wrote: >> >>> Hello, >>> >>> I am using the oligo package to work with tiling arrays. >>> >>> I was wondering if there is a way to either: >>> >>> 1. See how the pmindex function in oligo is calculating the >>> indices? >>> or >>> 2. Obtain the actual x,y coordinates for each probe? >>> >>> I found the functions indices2xy and xy2indices in the affy >>> package, but can't seem to find an equivalent function in oligo. >>> >>> Any advise would be greatly appreciated. My session info is >>> below, in case it is helpful. >>> >>> Thanks! >>> -Gayla Olbricht >>> >>> _______________________ >>>> sessionInfo() >>> R version 2.6.0 (2007-10-03) >>> x86_64-redhat-linux-gnu >>> >>> locale: >>> LC_CTYPE = en_US .UTF -8 ;LC_NUMERIC = C ;LC_TIME = en_US .UTF >>> -8 ;LC_COLLATE = en_US .UTF -8 ;LC_MONETARY = en_US .UTF >>> -8 ;LC_MESSAGES = en_US .UTF -8 ;LC_PAPER = en_US .UTF -8 ;LC_NAME >>> = C ;LC_ADDRESS >>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] splines tools stats graphics grDevices utils >>> datasets >>> [8] methods base >>> >>> other attached packages: >>> [1] pd.at35b.mr.v04_1.0.0 oligo_1.2.1 oligoClasses_1.0.3 >>> [4] affxparser_1.10.1 AnnotationDbi_1.0.6 preprocessCore_1.0.0 >>> [7] RSQLite_0.6-3 DBI_0.2-4 Biobase_1.16.1 >>> >>> loaded via a namespace (and not attached): >>> [1] rcompgen_0.1-15 >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor