[BioC] warning message of lumiR

[Pan Du]

Hi Merja,

These warning messages are not a problem.

For the first warning message, it is because you included "lumiHumanAll.db"
in the lumiR. For the new version of lumi Annotation packages, like
"lumiHumanAll.db", they do not include ID mapping information, so you don't
need to include it in the lumiR (see example in the new version of
vignette). You just need to type:
 rawX=lumiR("Raw_data.txt")
The lumiR function will automatically convert the probe sequences (if exist)
as nuIDs. 

For the second warning message, it is because Illumina gave different IDs
for the same probe sequence. In this case, lumiR will average them
(basically there are more beads for the same probe). So it is not a problem.



Pan


On 5/13/08 11:14 AM, "Merja Heinaniemi" <merja.heinaniemi at uni.lu> wrote:

> Hi again,
> 
> Sorry, I meant to include this in my previous email. I got a warning message
> when I loaded the actual data but it seems still that I have probes with
> NuIDs. So can you tell me what the message is trying to tell me?
> 
> Merja
> 
>> rawX=lumiR("Raw_data.txt", lib="lumiHumanAll.db")
> Directly converting probe sequence to nuIDs ...Warning messages:
> 1: In addNuId2lumi(x.lumi, lib = lib) :
>   lumiHumanAll.db does not include nuID conversion information!
> 2: In addNuId2lumi(x.lumi, lib = lib) :
>   Duplicated IDs found and were merged!
>> rawX
> Summary of BeadStudio output:
> 
> Major Operation History:
>             submitted            finished
> command lumiVersion
> 1 2008-05-13 09:44:55 2008-05-13 09:45:17    lumiR("Raw_data.txt", lib =
> "lumiHumanAll.db")       1.6.0
> 2 2008-05-13 09:45:17 2008-05-13 09:45:18 lumiQ(x.lumi = x.lumi, detectionTh =
> detectionTh)       1.6.0
> 3 2008-05-13 09:45:29 2008-05-13 09:45:30                        Subsetting
> 48804 features.       1.6.0
> 4 2008-05-13 09:45:18 2008-05-13 09:45:30          addNuId2lumi(x.lumi =
> x.lumi, lib = lib)       1.6.0
> 
> Object Information:
> LumiBatch (storageMode: lockedEnvironment)
> assayData: 48802 features, 18 samples
>   element names: beadNum, detection, exprs, se.exprs
> phenoData
>   sampleNames: dmso4n1, dmso4n2, ..., rosi24n3  (18 total)
>   varLabels and varMetadata description:
>     sampleID: The unique Illumina microarray Id
> featureData
>   featureNames: 9g8cQB1TZtuiix.ulU, fJUdX0IAn_P9VLTgJU, ...,
> N8t5EuJCr0Tk9.zHno  (48802 total)
>   fvarLabels and fvarMetadata description:
>     ProbeID: The Illumina microarray identifier
>     TargetID: The Illumina TargetID
>     ...: ...
>     DEFINITION: DEFINITION
>     (9 total)
> experimentData: use 'experimentData(object)'
> Annotation: Homo sapiens
> Control Data: Available
>