[BioC] Problem with new lumi/addNuID2lumi and old data
cei at ebi.ac.uk
Mon Oct 27 22:28:00 CET 2008
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:
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)
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
The provided library might be wrong or outdated!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!
-- sessionInfo() --
R version 2.8.0 (2008-10-20)
attached base packages:
 stats graphics grDevices datasets tools utils methods
other attached packages:
 lumiMouseIDMapping.db_1.0.0 lumi_1.8.2
 RSQLite_0.7-1 DBI_0.2-4
 preprocessCore_1.4.0 mgcv_1.4-1
 affy_1.20.0 annotate_1.20.0
 xtable_1.5-4 AnnotationDbi_1.4.0
loaded via a namespace (and not attached):
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