To whom it may concern, I am using R 2.9.1 in Linux (Ubuntu - Hardy). I have successfully installed 'affy' and it's dependencies. I am using a toy array dataset to make sure that I can analyse these arrays using affy. The data consists of 15 arrays (GeneChip Human Gene 1.0 ST Arrays). I have successfully read these arrays into my R workspace (I created the cdfpackage from the human gene st cdf file from affymetrix using makecdfenv): > Data AffyBatch object size of arrays=1050x1050 features (10 kb) cdf=hugenestcdf (33252 affyids) number of samples=15 number of genes=33252 annotation=hugenestcdf notes= I want to be able to create a boxplot and MAplot as described in the 'affy' primer pdf given on bioconductor (I am able to do this with the Dilution data provided on bioconductor) but when I try this on my 'Data' I get the following errors: > boxplot(Data) Error in data.frame(log2(intensity(x)[tmp, ])) : row names contain missing values In addition: Warning message: In data.frame(log2(intensity(x)[tmp, ])) : NAs introduced by coercion Error in boxplot(data.frame(log2(intensity(x)[tmp, ])), main = main, range = range, : error in evaluating the argument 'x' in selecting a method for function 'boxplot' > MAplot(Data) Error in .local(object, ...) : subscript out of bounds In addition: Warning message: In .local(object, ...) : NAs introduced by coercion When trying to fitPLM to the data I also get the following error: > library('affyPLM') Loading required package: gcrma Loading required package: matchprobes Loading required package: splines Loading required package: preprocessCore Attaching package: 'affyPLM' The following object(s) are masked from package:stats : resid, residuals, weights > plm.data <- fitPLM(Data) Error in .local(object, ...) : subscript out of bounds In addition: Warning message: In .local(object, ...) : NAs introduced by coercion I don't know what the errors mean or how to fix the problem so that I can analyse the data. Can 'affy' be used to analyse the Human Gene 1.0 ST array? Thank you very much Cathrine Mitchell [[alternative HTML version deleted]]

have a look at http://www.bioconductor.org/docs/workflows/oligoarrays/ you will find the entry Affymetrix Gene ST Arrays oligo * Requires a pdInfoPackage built using pdInfoBuilder * This package collates cdf, probe, annotation data together * These packages are available from Bioconductor via biocLite() xps * Requires installation of ROOT * Uses data files from Affymetrix (.CDF, .PGF, .CLF, .CSV) directly specifically, if you go the oligo route, you will need pd.hugene.1.0.st.v1 so that oligo read.celfiles will work for import the resulting object can be processed with oligo::rma you may also find hugene1.0stprobeset.db or hugene1.0sttranscriptcluster.db packages useful for annotation. have a look at the ArrayTools package as well. On Wed, Jul 29, 2009 at 5:55 AM, Cathrine Mitchell<cathrine.mitchell at="" simugen-global.com=""> wrote: > To whom it may concern, > > I am using R 2.9.1 in Linux (Ubuntu - Hardy). I have successfully installed > 'affy' and it's dependencies. > I am using a toy array dataset to make sure that I can analyse these arrays > using affy. > The data consists of 15 arrays (GeneChip Human Gene 1.0 ST Arrays). > I have successfully read these arrays into my R workspace (I created the > cdfpackage from the human gene st cdf file from affymetrix using > makecdfenv): > >> Data > AffyBatch object > size of arrays=1050x1050 features (10 kb) > cdf=hugenestcdf (33252 affyids) > number of samples=15 > number of genes=33252 > annotation=hugenestcdf > notes= > > > I want to be able to create a boxplot and MAplot as described in the 'affy' > primer pdf given on bioconductor (I am able to do this with the Dilution > data provided on bioconductor) but when I try this on my 'Data' I get the > following errors: > >> boxplot(Data) > Error in data.frame(log2(intensity(x)[tmp, ])) : > ?row names contain missing values > In addition: Warning message: > In data.frame(log2(intensity(x)[tmp, ])) : NAs introduced by coercion > Error in boxplot(data.frame(log2(intensity(x)[tmp, ])), main = main, range = > range, ?: > ?error in evaluating the argument 'x' in selecting a method for function > 'boxplot' > > ?> MAplot(Data) > Error in .local(object, ...) : subscript out of bounds > In addition: Warning message: > In .local(object, ...) : NAs introduced by coercion > > > When trying to fitPLM to the data I also get the following error: > >> library('affyPLM') > Loading required package: gcrma > Loading required package: matchprobes > Loading required package: splines > Loading required package: preprocessCore > > Attaching package: 'affyPLM' > > > ? ?The following object(s) are masked from package:stats : > > ? ? resid, > ? ? residuals, > ? ? weights > >> plm.data <- fitPLM(Data) > Error in .local(object, ...) : subscript out of bounds > In addition: Warning message: > In .local(object, ...) : NAs introduced by coercion > > > I don't know what the errors mean or how to fix the problem so that I can > analyse the data. Can 'affy' be used to analyse the Human Gene 1.0 ST array? > > > Thank you very much > > Cathrine Mitchell > > ? ? ? ?[[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 > -- Vincent Carey, PhD Biostatistics, Channing Lab 617 525 2265