Hi,

I am trying to filter my probes based on the quality score, but it gives me an error. I ran the script few times. It was previously working. When I try to run the script in "BeadArrayUseCases.pdf" using the demo dataset, it also gives the same error. What could be the reason?


These are the commands that I am using for my dataset:

data <- read.ilmn(files="MEF triangle_Sample_Probe_Profile.txt",ctrlfiles="MEF triangle_Control_Probe_Profile.txt",
probeid="ProbeID", annotation="TargetID", other.columns="Detection")
data.cor <- nec(data)
library(illuminaMousev2.db)
illuminaMousev2()
ids <- as.character(rownames(data.cor))
ids2 <- unlist(mget(ids,revmap(illuminaMousev2ARRAYADDRESS),
ifnotfound=NA))
qual <- unlist(mget(ids2,illuminaMousev2PROBEQUALITY,
ifnotfound=NA))

This is the error:
"Error in .checkKeysAreWellFormed(keys) :
  keys must be supplied in a character vector with no NAs"

Here is the session info:
R version 2.15.2 (2012-10-26)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] illuminaHumanv2.db_1.16.0 org.Hs.eg.db_2.8.0
 [3] BiocInstaller_1.8.3       illuminaMousev2.db_1.16.1
[5] org.Mm.eg.db_2.8.0        RSQLite_0.11.2
 [7] DBI_0.2-5                 AnnotationDbi_1.20.3
 [9] Biobase_2.18.0            BiocGenerics_0.4.0
[11] limma_3.14.3

loaded via a namespace (and not attached):
[1] AnnotationForge_1.0.3 IRanges_1.16.4        parallel_2.15.2
[4] stats4_2.15.2         tools_2.15.2


Thank you,

Gaye

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