Hello everybody! I am not sure if this is the way for asking because I am new in this kind of "help-website" so, please if I am wrong tell me. I am trying to make a cdf package for the Human Exon Array chip from Affymetrix (HuEx-1_0-st-v2). I have downloaded the file HuEx-10-st-v2.cdf from the Affymetrix website and write the following commands in the R program: library(makecdfenv) pkgpath<-tempdir() make.cdf.package("HuEx-1_0-st-v2.text.cdf",cdf.path="/Working/HuEx- 1_0-st-v2.r2",compress=F, species = "Homo_sapiens", package.path = pkgpath) It costs me a lot of time and most of the RAM memory of my computer and at the end the following message appears: Reading CDF file. Error in .Call("reaD file", as.character(file), as.integer(3), as.integer(compress), :promise already under evaluation: recursive default argument reference or earlier problems? I have no idea if I am doing anything wrong or if there is a better method for making the package, so any help will be really welcome. Thank you, Maria -- output of sessionInfo(): R version 2.15.3 (2013-03-01) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] makecdfenv_1.36.0 loaded via a namespace (and not attached): [1] affy_1.36.1 affyio_1.26.0 Biobase_2.18.0 [4] BiocGenerics_0.4.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 [7] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.

Hi Maria, On 4/4/2013 11:44 AM, Maria [guest] wrote: > Hello everybody! > > I am not sure if this is the way for asking because I am new in this kind of "help-website" so, please if I am wrong tell me. You asked your question perfectly! Nice work. > > I am trying to make a cdf package for the Human Exon Array chip from Affymetrix (HuEx-1_0-st-v2). I have downloaded the file HuEx-10-st-v2.cdf from the Affymetrix website and write the following commands in the R program: > > library(makecdfenv) > pkgpath<-tempdir() > make.cdf.package("HuEx-1_0-st-v2.text.cdf",cdf.path="/Working/HuEx- 1_0-st-v2.r2",compress=F, species = "Homo_sapiens", package.path = pkgpath) > > It costs me a lot of time and most of the RAM memory of my computer and at the end the following message appears: > > Reading CDF file. > Error in .Call("reaD file", as.character(file), as.integer(3), > as.integer(compress), :promise already under evaluation: recursive default > argument reference or earlier problems? > > I have no idea if I am doing anything wrong or if there is a better method for making the package, so any help will be really welcome. You are doing something wrong - the makecdfenv package isn't designed for these types of arrays, which is why it failed. To analyze exon arrays, you have two choices. You can either use the oligo or xps package. I am unfamiliar with xps, but Christian Stratowa, the author of that package is very helpful. I am more familiar with oligo. For this package you can just load the package and then do something like dat <- read.celfiles(list.celfiles()) assuming you started R in the same directory that contains your celfiles. Otherwise you need to add in path information so these functions can find the files. You can then do eset <- rma(dat) and depending on the goals of your analysis, you can select the level at which you want to summarize your data. See ?rma for more information. Best, Jim > > Thank you, > > Maria > > -- output of sessionInfo(): > > R version 2.15.3 (2013-03-01) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > [2] LC_CTYPE=English_United Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] makecdfenv_1.36.0 > > loaded via a namespace (and not attached): > [1] affy_1.36.1 affyio_1.26.0 Biobase_2.18.0 > [4] BiocGenerics_0.4.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 > [7] zlibbioc_1.4.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

Hi Maria, A quick glance at the PREDA vignette indicates to me that you can use already processed data. See e.g., page 7-8 of the PREDAtutorial, and ?statisticsForPREDAfromEset. Best, Jim On 4/4/2013 1:20 PM, Maria Arnedo Munoz wrote: > Hi Jim! > > The problem is that I really need to build a cdf environment in order > to analyse these arrays with the PREDA package and when I look for it > in the bioconductor website I can't find it because it isn't there. > > I am trying to compare the gene expression between two different cell > lines but not focus in specific genes, I like to know if there are > huge (or big enough) chromosome regions with different gene expression > between the two cell lines (the PREDA package makes this kind of > analyses), and the only array that I have found for both is a HuEx. > > So, does anyone know how to do that? If it isn't possible I will try > to analyse with another package that makes the same kind of analyses. > > Thank you > > Best > > Maria > > Quoting "James W. MacDonald" <jmacdon at="" uw.edu=""> on Thu, 04 Apr 2013 > 11:56:58 -0400: > >> Hi Maria, >> >> On 4/4/2013 11:44 AM, Maria [guest] wrote: >>> Hello everybody! >>> >>> I am not sure if this is the way for asking because I am new in this >>> kind of "help-website" so, please if I am wrong tell me. >> >> You asked your question perfectly! Nice work. >> >>> >>> I am trying to make a cdf package for the Human Exon Array chip from >>> Affymetrix (HuEx-1_0-st-v2). I have downloaded the file >>> HuEx-10-st-v2.cdf from the Affymetrix website and write the >>> following commands in the R program: >>> >>> library(makecdfenv) >>> pkgpath<-tempdir() >>> make.cdf.package("HuEx-1_0-st-v2.text.cdf",cdf.path="/Working /HuEx-1_0-st-v2.r2",compress=F, >>> species = "Homo_sapiens", package.path = pkgpath) >>> >>> It costs me a lot of time and most of the RAM memory of my computer >>> and at the end the following message appears: >>> >>> Reading CDF file. >>> Error in .Call("reaD file", as.character(file), as.integer(3), >>> as.integer(compress), :promise already under evaluation: recursive >>> default >>> argument reference or earlier problems? >>> >>> I have no idea if I am doing anything wrong or if there is a better >>> method for making the package, so any help will be really welcome. >> >> You are doing something wrong - the makecdfenv package isn't designed >> for these types of arrays, which is why it failed. To analyze exon >> arrays, you have two choices. You can either use the oligo or xps >> package. I am unfamiliar with xps, but Christian Stratowa, the author >> of that package is very helpful. >> >> I am more familiar with oligo. For this package you can just load the >> package and then do something like >> >> dat <- read.celfiles(list.celfiles()) >> >> assuming you started R in the same directory that contains your >> celfiles. Otherwise you need to add in path information so these >> functions can find the files. You can then do >> >> eset <- rma(dat) >> >> and depending on the goals of your analysis, you can select the level >> at which you want to summarize your data. See ?rma for more information. >> >> Best, >> >> Jim >> >> >>> >>> Thank you, >>> >>> Maria >>> >>> -- output of sessionInfo(): >>> >>> R version 2.15.3 (2013-03-01) >>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_United Kingdom.1252 >>> [2] LC_CTYPE=English_United Kingdom.1252 >>> [3] LC_MONETARY=English_United Kingdom.1252 >>> [4] LC_NUMERIC=C >>> [5] LC_TIME=English_United Kingdom.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] makecdfenv_1.36.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affy_1.36.1 affyio_1.26.0 Biobase_2.18.0 >>> [4] BiocGenerics_0.4.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 >>> [7] zlibbioc_1.4.0 >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> 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 >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> > > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099