Hi, I am trying to use the summarize function in beadarray to grouped together beadLevelData object according to their ArrayAddressID. I have data from Illumina Human660w_quad bead chip. I didn't specified the annotation when using the readIllumina function because my platform is not among the options that show up when using the suggestAnnotation function. I have successfully read in the data using the readIllumina function. I am hoping that I can use the summarize function without having to specified the annotation. Below is the message I get when using the summarize function and the traceback function. Any suggestion on how to fix this error with be greatly appreciated. thanks, Anna > datasum <- summarize(data, removeUnMappedProbes= FALSE) No sample factor specified. Summarizing each section separately Finding list of unique probes in beadLevelData 210732 unique probeIDs found Summarizing G channel Processing Array 1 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 2 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 3 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 4 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 5 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 6 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 7 Removing outliers Using exprFun Using varFun Summarizing G channel Processing Array 8 Removing outliers Using exprFun Using varFun Making summary object Could not map ArrayAddressIDs: No annotation specified Error in value[[3L]](cond) : row names supplied are of the wrong length AnnotatedDataFrame 'initialize' could not update varMetadata: perhaps pData and varMetadata are inconsistent? > traceback() 10: stop(conditionMessage(err), "\n AnnotatedDataFrame 'initialize' could not update varMetadata:", "\n perhaps pData and varMetadata are inconsistent?") 9: value[[3L]](cond) 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, handlers) 6: tryCatch({ if (missing(varMetadata)) { if (!missing(data)) checkClass(data, "data.frame", class(.Object)) varMetadata <- data.frame(labelDescription = rep(NA, ncol(data))) row.names(varMetadata) <- as.character(colnames(data)) } else { checkClass(varMetadata, "data.frame", class(.Object)) if (!"labelDescription" %in% colnames(varMetadata)) varMetadata[["labelDescription"]] <- rep(NA, nrow(varMetadata)) row.names(varMetadata) <- names(data) } varMetadata[["labelDescription"]] <- as.character(varMetadata[["labelDescription"]]) }, error = function(err) { stop(conditionMessage(err), "\n AnnotatedDataFrame 'initialize' could not update varMetadata:", "\n perhaps pData and varMetadata are inconsistent?") }) 5: .local(.Object, ...) 4: initialize(value, ...) 3: initialize(value, ...) 2: new("AnnotatedDataFrame", data.frame(sampInfo, row.names = newNames)) 1: summarize(data, removeUnMappedProbes = FALSE) > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_2.6.0 ggplot2_0.9.1 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.18.1 BeadDataPackR_1.8.0 colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 grid_2.15.0 [8] IRanges_1.14.3 labeling_0.1 limma_3.12.1 MASS_7.3-18 memoise_0.1 munsell_0.3 plyr_1.7.1 [15] proto_0.3-9.2 RColorBrewer_1.0-5 reshape2_1.2.1 RSQLite_0.11.1 scales_0.2.1 stats4_2.15.0 stringr_0.6 [22] tools_2.15.0