I'm working with some data sets which have several platforms, but would like to just work with data from one platform at a time. The code below does NOT work, but it is where I'm at. Can somebody give me a hint on how to modify the lapply() to do what i would like? Thanks, Jeremiah ---------------- library(GEOquery) geodata <- parseGEO("GSE5720.soft") gplnames <- names(GPLList(geodata)) j <- 1 while(j <= length(gplnames)) { gsmdata <- lapply(GSMList(geodata), function(x) { gplnames[j] == Meta(x)$platform_id # this line does nothing, # I would like to alter it so only # one platform is applied. }) # would like 'gsmdata' to now hold half of data # in 'geodata', but it holds all of the data j <- j+1 } [[alternative HTML version deleted]]

I've worked around this problem by doing the following: gplnames <- names(GPLList(geodata)) numgpl <- length(gplnames) gsmdata <- GSMList(geodata) j <- 1 while(j <= numgpl) { accumgsm <- list() for(i in gsmdata) { if(gplnames[j] == Meta(i)$platform_id) accumgsm <- append(accumgsm, i) } j <- j + 1 } On Mon, Jun 28, 2010 at 12:56 PM, Jeremiah H. Savage < jeremiahsavage@gmail.com> wrote: > I'm working with some data sets which have several platforms, but would > like to just work with data from one platform at a time. > > The code below does NOT work, but it is where I'm at. Can somebody give me > a hint on how to modify the lapply() to do what i would like? > > Thanks, > Jeremiah > > > ---------------- > library(GEOquery) > geodata <- parseGEO("GSE5720.soft") > gplnames <- names(GPLList(geodata)) > j <- 1 > while(j <= length(gplnames)) > { > gsmdata <- lapply(GSMList(geodata), function(x) { > gplnames[j] == Meta(x)$platform_id # this line does nothing, > # I would like to alter it so only > # one platform is applied. > }) > > # would like 'gsmdata' to now hold half of data > # in 'geodata', but it holds all of the data > j <- j+1 > } > > [[alternative HTML version deleted]]

On Mon, Jun 28, 2010 at 3:56 PM, Jeremiah H. Savage < jeremiahsavage@gmail.com> wrote: > I'm working with some data sets which have several platforms, but would > like > to just work with data from one platform at a time. > > Hi, Jeremiah. library(GEOquery) gsedat = getGEO("GSE5720") names(gsedat) [1] "GSE5720-GPL96_series_matrix.txt.gz" "GSE5720-GPL97_series_matrix.txt.gz" gsedat[[1]] is, then, and ExpressionSet and includes only GPL96 platform data. gsedat[[2]] is an ExpressionSet and contains only GPL97 data. Hope that helps. Sean > The code below does NOT work, but it is where I'm at. Can somebody give me > a > hint on how to modify the lapply() to do what i would like? > > Thanks, > Jeremiah > > > ---------------- > library(GEOquery) > geodata <- parseGEO("GSE5720.soft") > gplnames <- names(GPLList(geodata)) > j <- 1 > while(j <= length(gplnames)) > { > gsmdata <- lapply(GSMList(geodata), function(x) { > gplnames[j] == Meta(x)$platform_id # this line does nothing, > # I would like to alter it so only > # one platform is applied. > }) > > # would like 'gsmdata' to now hold half of data > # in 'geodata', but it holds all of the data > j <- j+1 > } > > [[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 > [[alternative HTML version deleted]]