[BioC] beadarray package: get error message when using summarize function

[bzguan at ucdavis.edu]

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