Hi Lavinia,

Before combining tow dataset of different Illumina chip versions, you need
to convert them as the same type of IDs (nuID is a good option provided in
the lumi package). Then you should subset the datasets by using the common
IDs before combining them.

Here is one example:
Suppose you have two LumiBatch objects: x.lumi1 and x.lumi2 of Human
Illumina chips, you can use the following code:

  x.lumi1 = addNuID2lumi(x.lumi1, lib=šlumiHumanIDMappingš)
 x.lumi2 = addNuID2lumi(x.lumi2, lib=šlumiHumanIDMappingš)
 commonID = intersect(featureNames(x.lumi1), featureNames(x.lumi2))
 x.lumi.combine = combine(x.lumi1[commonID,], x.lumi2[commonID,])

If the library šlumiHumanIDMappingš cannot be install through biocLite(),
you can also use library šlumiHumanIDMapping.dbš. These two libraries
basically are the same. Also you need to use R 2.8.

Tell me if you have further questions.

 
Pan


On 11/13/08 7:00 PM, "Lavinia Gordon" <lavinia.gordon@mcri.edu.au> wrote:

> Hi Pan,
> 
> I tried to send this email to the Bioconductor list but for some reason it
> didn't appear properly on the mailing list.  I wondered if you might be able
> to help, as I am sure that it is a question that others have asked.
> 
> with thanks for your time,
> 
> Lavinia Gordon.
> 
>> Date: Thu, 13 Nov 2008 15:11:26 +1100
>> To: bioconductor@stat.math.ethz.ch
>> From: Lavinia Gordon <lavinia.gordon@mcri.edu.au>
>> Subject: Illumina arrays - combining two versions.
>> 
>> Dear all,
>> 
>> I have two sets of data, both generated on Illumina BeadArrays, but on two
>> different versions of the array (the newer version has slightly more probes).
>> I would like to normalize these two array types together in lumi, does anyone
>> know if/how this can be done?
>> 
>> with thanks for your time,
>> 
>> Lavinia Gordon.
>> 
>> -------------------------------------------------------
>> Bioinformatics Department
>> Rm SW916, 9th Floor
>> Murdoch Children's Research Institute
>> Royal Children's Hospital
>> Flemington Road, Parkville
>> Victoria 3052
>> Australia
>> Tel: (+613) 8341 6221
>> -------------------------------------------------------
> -------------------------------------------------------
> Bioinformatics Department
> Rm SW916, 9th Floor
> Murdoch Children's Research Institute
> Royal Children's Hospital
> Flemington Road, Parkville
> Victoria 3052
> Australia
> Tel: (+613) 8341 6221
> -------------------------------------------------------





	[[alternative HTML version deleted]]

