Goodmorning, I am new to the list, as well as to R and Bioconductor. As I work through the R manual, texts, and related book chapters; I have encountered a problem trying to walk through the examples in Gentleman and Carey's chapter "Visualization and Annotation of Genomic Experiments". I am runing the examples on a Win2000 machine under R 1.7 and Bioconductor 1.2. I have downloaded the *.rda files from the Springer website into a data directory on my C: drive. I load() the golubTrain.rda and golubTest.rda along with the appropriate libraries--biobase, genefilter, and annotate. Typing golubTrain yields the description of the R data object. The problem I am encountering is with commands that involving indexing: e.g., golubTrain[1:4,] or the print() command. The former returns only the descrition of the R data object and the latter returns "NULL". I must be missing an important step. Can some one help me? John

> Goodmorning, > > I am new to the list, as well as to R and Bioconductor. As I work through > the R manual, texts, and related book chapters; I have encountered a problem > trying to walk through the examples in Gentleman and Carey's chapter > "Visualization and Annotation of Genomic Experiments". I am runing the > examples on a Win2000 machine under R 1.7 and Bioconductor 1.2. I have > downloaded the *.rda files from the Springer website into a data directory > on my C: drive. I load() the golubTrain.rda and golubTest.rda along with > the appropriate libraries--biobase, genefilter, and annotate. Typing > golubTrain yields the description of the R data object. The problem I am > encountering is with commands that involving indexing: e.g., > golubTrain[1:4,] or the print() command. The former returns only the > descrition of the R data object and the latter returns "NULL". I must be > missing an important step. Can some one help me? golubTrain is an instance of a class called "exprSet". some salient features of exprSets 1) they combine expression and phenotype data 2) they can be subscripted like matrices 3) the 'show' method is designed to avoid dumps of massive volumes of data to the screen 4) special accessor methods are available to permit manual exploration of the data > golubTrain[1:4,] Expression Set (exprSet) with 4 genes 38 samples phenoData object with 11 variables and 38 cases varLabels Samples: Sample index ALL.AML: Factor, indicating ALL ... now admittedly the above looks like the result of mentioning golubTrain (simpliciter) to the interpreter ... but note the number of genes in this expression set. This shows the convention for subscripting with this special data structure: row subscripting selects genes. > golubTrain[,1:4] Expression Set (exprSet) with 7129 genes 4 samples phenoData object with 11 variables and 4 cases varLabels Samples: Sample index ALL.AML: Factor, indicating .... column subscripting selects 'samples' or bearers of phenotype data. it seems that your objective was to look at some expression values. to do this, use the exprs accessor function: > exprs(golubTrain)[1:4,1:5] [,1] [,2] [,3] [,4] [,5] AFFX-BioB-5_at -214 -139 -76 -135 -106 AFFX-BioB-M_at -153 -73 -49 -114 -125 AFFX-BioB-3_at -58 -1 -307 265 -76 AFFX-BioC-5_at 88 283 309 12 168 named subscripting also works: > exprs(golubTrain)[c("AFFX-BioB-5_at", "AFFX-BioB-M_at"),] [,1] [,2] [,3] [,4] [,5] AFFX-BioB-5_at -214 -139 -76 -135 -106 AFFX-BioB-M_at -153 -73 -49 -114 -125 this allows you to extract expressions for specific probes if desired, by name. I couldn't reproduce your finding of "NULL". tell me more about how you were using "print"