Hi BioC, When calling function nsFilter() from package 'genefilter' on an "ExpressionSetIllumina"data object from package, 'beadarray', I get the following errors, and I am not sure why?: > nsFilter(eSet.illumina) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "nsFilter", for signature "ExpressionSetIllumina" RE: I am trying to filter-out low varying probes from my expression data to make my "gene universe" a minimal set prior to performing hypergeometric testing of GO terms. Here is some object info regarding the session data object I am working with, 'eSet.illumina': (Note: I am using function readBeadSummaryData() from package 'beadarray' to read-in my raw bead summary data file, 'sample_probe_profile.txt'; details of session object construction shown at bottom) # print object class > class(eSet.illumina) [1] "ExpressionSetIllumina" attr(,"package") [1] "beadarray" # print object dimensions > dim(eSet.illumina) Features Samples 22517 48 # subset object > eSet.illumina[1:2,2:5] Error: subscript out of bounds ..., I found that creating an ExpressionSet object from scratch, somehow fixes the subsetting error, > exprs.illumina <- exprs(eSet.illumina) > minimalSet <- new("ExpressionSet", exprs=exprs.illumina, annotation="illuminaRatv1BeadID.db") > minimalSet[1:2,2:5] ExpressionSet (storageMode: lockedEnvironment) assayData: 2 features, 4 samples element names: exprs phenoData sampleNames: 1677718209_B, 1677718209_C, 1677718209_D, 1677718209_E varLabels and varMetadata description: none featureData featureNames: 4560377, 5860059 fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: illuminaRatv1BeadID.db ..., but when I call nsFilter() on my new minimal ExpressionSet object, I get a different error: > nsFilter(minimalSet) Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : value for "4010324" not found e.g., You can replicate the nsFilter() .checkKeys() error by using the data from, [ http://www.compbio.group.cam.ac.uk/Resources/illumina/BeadSummaryExamp le.zip ] and using the annotation package, illuminaHumanv1BeadID.db And finally, I constructed my local session ExpressionSetIllumina data object, 'eSet.illumina' by doing, # library setup > library(beadarray) > library(illuminaRatv1BeadID.db) > library(genefilter) # --- # show BeadStudio version for file, 'sample_probe_profile.txt' # --- # Illumina Inc. BeadStudio version 2.3.47 # Normalization = none # Array Content = RatRef_12_v1_11222119_A.xml.xml # Error Model = none # read-in bead summary data file using function # readBeadSummaryData() from package 'beadarray': > dataFile <- "./sample_probe_profile.txt" > eSet.illumina <- readBeadSummaryData( dataFile, + skip = 7, + columns = list( exprs = "AVG_Signal", + se.exprs = "BEAD_STDEV", + NoBeads = "Avg_NBEADS", + Detection = "Detection" + ), + annoPkg = "illuminaRatv1BeadID.db" + ) * What am I missing here? Thank you, Elliot Kleiman # print SessionInfo() > sessionInfo() R version 2.9.0 (2009-04-17) i686-pc-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=C;L C_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C; LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] genefilter_1.24.0 illuminaRatv1BeadID.db_1.2.0 [3] RSQLite_0.7-1 DBI_0.2-4 [5] AnnotationDbi_1.6.0 beadarray_1.12.0 [7] sma_0.5.15 hwriter_1.1 [9] Biobase_2.4.1 loaded via a namespace (and not attached): [1] annotate_1.22.0 limma_2.18.0 splines_2.9.0 survival_2.35-4 [5] tools_2.9.0 xtable_1.5-5 -- MS graduate student Computational Science Program San Diego State University http://www.csrc.sdsu.edu/ http://www.sdsu.edu/