[BioC] BeadArray

[Mark Dunning]

Hi Gaye,

Unfortunately, it looks as though this version of the
illuminaHumanv2.db package has some missing probe mappings, which is
causing you to get some NA values when you do the first lookup. The
packages will have to be re-built and uploaded, which will take a day
or so.

For now, you can add an explicit check for NA values before you look
up the probe qualities.

ids2 <- unlist(mget(ids, revmap(illuminaHumanv2ARRAYADDRESS), ifnotfound=NA))

ids2 <- ids2[-which(is.na(ids2))]

qual <- unlist(mget(ids2, illuminaHumanv2PROBEQUALITY, ifnotfound=NA))

table(qual)

AveSignal = rowMeans(maqc.norm$E[as.character(names(ids2)),])

boxplot(AveSignal~ qual)

rem <- qual == "No match" | qual == "Bad"

maqc.norm.filt <- maqc.norm[unlist(mget(names(qual)[!rem],
illuminaHumanv2ARRAYADDRESS)),]

Sorry for the inconvenience,

Mark
On Mon, Jan 14, 2013 at 6:40 AM, Gaye SAGINC (GIS)
<sagincg99 at gis.a-star.edu.sg> wrote:
> 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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