Hi List, I'm pretty new to R and BioConductor, but am trying to use Affy to process my CEL files for analysis. I understand the first step to doing this is to do an RMA normalization. Further, I used the ram argument in Affy to to an RMA normalization. however, the following error message gets returned: "Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuEx-1_0-st-v2 Library - package huex10stv2cdf not installed Bioconductor - huex10stv2cdf not available" The codes I used are as follows, after setting my working directory to the location of my CEL files: >library(affy) >c<- read.Affy() Once my CEL files (4 of them) have been read in, I attempted to run the RMA by invoking: >r<- rma(c, verbose=TRUE, normalization=TRUE, background=TRUE). Invoking this lead to the error message concerning the CDF environment issue. May I inquire as to how I can go about rectifying this? This is my session info: R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/en_US.UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] affy_1.36.0 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] BiocInstaller_1.8.2 affyio_1.26.0 preprocessCore_1.20.0 [4] tools_2.15.1 zlibbioc_1.4.0 May I also ask for some suggestions on what kind of workflow should I follow? I'm interested in annotating alternative splicing events. Thanks a ton in advance! Jeremy [[alternative HTML version deleted]]

On Wed, Oct 17, 2012 at 8:06 AM, Jeremy Ng <jeremy.ng.wk1990@gmail.com>wrote: > Hi List, > > I'm pretty new to R and BioConductor, but am trying to use Affy to process > my CEL files for analysis. > > I understand the first step to doing this is to do an RMA normalization. > Further, I used the ram argument in Affy to to an RMA normalization. > however, the following error message gets returned: > > "Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuEx-1_0-st-v2 > Library - package huex10stv2cdf not installed > Bioconductor - huex10stv2cdf not available" > > Hi, Jeremy. It looks like you are trying to work with HuEx arrays. Take a look here: http://www.bioconductor.org/help/workflows/oligo-arrays/#pre- processing-resources In particular, you will probably want to use the oligo package (or another on that list). The affy package is for 3' pm/mm arrays. Hope that helps. Sean The codes I used are as follows, after setting my working directory to the > location of my CEL files: > >library(affy) > >c<- read.Affy() > > Once my CEL files (4 of them) have been read in, I attempted to run the RMA > by invoking: > >r<- rma(c, verbose=TRUE, normalization=TRUE, background=TRUE). > > Invoking this lead to the error message concerning the CDF environment > issue. May I inquire as to how I can go about rectifying this? > > This is my session info: > R version 2.15.1 (2012-06-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C/en_US.UTF-8/C/C/C/C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > [7] base > > other attached packages: > [1] affy_1.36.0 Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] BiocInstaller_1.8.2 affyio_1.26.0 preprocessCore_1.20.0 > [4] tools_2.15.1 zlibbioc_1.4.0 > > May I also ask for some suggestions on what kind of workflow should I > follow? I'm interested in annotating alternative splicing events. > > Thanks a ton in advance! > > Jeremy > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]