Hello, I need to analyze a microarray dataset that used Human Gene 1.1 ST Array. When I ran following command lines: library(affy) library(limma) Data <- ReadAffy() I got this warning message and error: Warning message: The affy package can process data from the Gene ST 1.x series of arrays, but you should consider using either the oligo or xps packages, which are specifically designed for these arrays. > Data AffyBatch object size of arrays=1190x990 features (25 kb) cdf=HuGene-1_1-st-v1 (??? affyids) number of samples=20 Error in (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE, : ‘hugene11stv1cdf’ is not a valid installed package In addition: Warning message: missing cdf environment! in show(AffyBatch) May someone let me know how I could fix this problem? Thanks, Jerry [[alternative HTML version deleted]]

Hi Jerry, I am going to assume you saw and read the warning, considering you printed it out. It says that you should be using the oligo or xps packages. So that is step #1. Use one of those two packages instead of the affy package. There are vignettes for both packages that you can read to help you get started. Note that you can summarize the Gene ST arrays at either the transcript or probeset (roughly exon) level, so the annotation package you will need to map probesets to genes, etc, will either be the hugene11sttranscriptcluster.db or hugene11probeset.db package. Best, Jim On Tuesday, November 05, 2013 5:49:56 PM, Jerry Cholo wrote: > Hello, > > > > I need to analyze a microarray dataset that used Human Gene 1.1 ST Array. When > I ran following command lines: > > > > library(affy) > > library(limma) > > Data <- ReadAffy() > > > > I got this warning message and error: > > > > Warning message: > > > > The affy package can process data from the Gene ST 1.x series of arrays, > > but you should consider using either the oligo or xps packages, which are > specifically > > designed for these arrays. > > > >> Data > > AffyBatch object > > size of arrays=1190x990 features (25 kb) > > cdf=HuGene-1_1-st-v1 (??? affyids) > > number of samples=20 > > Error in (function (package, help, pos = 2, lib.loc = NULL, character.only > = FALSE, : > > ?hugene11stv1cdf? is not a valid installed package > > In addition: Warning message: > > missing cdf environment! in show(AffyBatch) > > > > May someone let me know how I could fix this problem? > > > > Thanks, > > Jerry > > [[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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099