[BioC] Problem with new lumi/addNuID2lumi and old data

[Cei Abreu-Goodger]

Hello Pan, et al,

As BioC gets updated, I've been having a lot of problems to be able to 
re-analyze old data. Particularly, I have data from the Mouse WG 6 v1_1 
read by BeadStudio version 3.0.14

I would like to still be able to use this data, but with the new 
annotation packages with NuIDs.

I currently get this error:
lumiR("Sample_Gene_Profile.txt", 
lib.mapping="lumiMouseIDMapping.db")
Annotation columns are not available in the data.
Perform Quality Control assessment of the LumiBatch object ...
Error in which(naInd) : argument to 'which' is not logical

I guess line 150 from the 'addNuID2lumi' should be:
             naInd <- is.na(newId)
instead of:
             naInd <- which(is.na(newId))

But after modifying this, I get another error:
Error in `[.data.frame`(pData(featureData), , "PROBE_SEQUENCE") :
   undefined columns selected

which I can avoid by removing lines 249 and 250.

In the end, I get the following warning, which makes me wonder if all the 
old target IDs are actually in the "lumiMouseIDMapping" file:
  More than 500 identifiers cannot be found in the 
library:lumiMouseIDMapping.db!
  The provided library might be wrong or outdated!

There are 658 TargetIDs that don't get converted: "lysA", "pheA", "thrB", 
"trpF" (controls) and the rest of the form: "GI_85986636-S"

Any suggestions are welcome!

Cei

-- sessionInfo() --

R version 2.8.0 (2008-10-20)
i386-apple-darwin8.11.1

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
  [1] lumiMouseIDMapping.db_1.0.0 lumi_1.8.2
  [3] RSQLite_0.7-1               DBI_0.2-4
  [5] preprocessCore_1.4.0        mgcv_1.4-1
  [7] affy_1.20.0                 annotate_1.20.0
  [9] xtable_1.5-4                AnnotationDbi_1.4.0
[11] Biobase_2.2.0

loaded via a namespace (and not attached):
[1] affyio_1.10.0