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

[Pan Du]

Hi Cei,

I guess the problem was caused by the newly added IDMapping procedure.
Probably some Target IDs of your data (maybe in different format) were not
included in the IDMapping package. Can you send me the data to have a check?
You can send the data to my gmail email (du4pan1 at gmail.com) if the data
is big. Thanks for reporting the problem.


Pan


On 10/28/08 6:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Date: Mon, 27 Oct 2008 21:28:00 +0000 (GMT)
> From: Cei Abreu-Goodger <cei at ebi.ac.uk>
> Subject: [BioC] Problem with new lumi/addNuID2lumi and old data
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <alpine.LRH.1.00.0810272103040.24596 at penguin.ebi.ac.uk>
> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
> 
> 
> 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   The provided library might be wrong or outdated!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
>