[BioC] About Illumina annotation packages lumixxxAll.db

Pan Du dupan at northwestern.edu
Fri May 2 23:00:38 CEST 2008

Hi Bob,

I guess the chip you use is Version 1.1 R2, which includes some new probes
not included in the old releases (lumiMouseV1 was based on version 1.1 R0
and version 1.0). 

 I am not sure how to output annotation information in the BeadStudio in our
microarray core here. I will check with them later. Another way is to unzip
the manifest file (.bgx), which basically is zipped by gzip. You can open
the unzipped file (basically it is a text file) and check whether there is a
probe sequence column. If so, you can use this file to convert the Ilumina
IDs as nuIDs by using:

 x.lumi = lumiR(filename, convertNuID=FALSE)
 x.lumi = addNuId2lumi(x.lumi,
annotationColName=c(sequence='Probe_Sequence', probe='Probe_Id'))

Here suppose 'MouseWG-6_V1_1_R2_11234304_A' is the manifest file you use.
Tell me if this does not work for you.

Have a nice weekend,


On 5/2/08 2:56 PM, "Robert Searles" <searlesr at ohsu.edu> wrote:

> Pan,
> Thanks for the quick reply and I apologize for being a nudge about
> this.  
> I'm using the most current version of BeadStudio and of the BeadStudio
> Gene Expression Module (I just verified this to be correct).  The data
> for the arrays is derived from the new .bgx files, not the old .csv
> files, though I don't think that has much relevance here.  BeadStudio
> v3.1.3 is not, by default, exporting the sequence data along with the
> rest of the data; at least my installation is not.
> Given that I'm using the newest software and manifests, I guess a
> better question for me to ask is "how do you output the correct data
> from BeadStudio?"  I've been using either the GeneSpring GX Group Probe
> Profile option or Sample Probe Profile on the File menu.  Is this the
> correct method or is this where I'm making my first mistake?  The data
> that I'm getting admittedly doesn't look like the example in the
> documentation - the header format is a bit different and the block
> designators don't come through at all.
> When I use lumiMouseV1 with the Mousev1.1 arrays, only the probeids
> that are also on the older V1 arrays are converted to nuIDs.  The new
> probes that occur only on the v1.1 array (about 2096 probes) instead
> retain their probeids.  So, when I convert the lumi.N file to an exprs
> object and output it using write.table, the first column is a mix of
> nuIDs (for 95% of the array) and probeids (the remaining 5% of the
> array).  On the off chance that my copy of lumiMouseV1 was outdated, I
> reloaded it and then also set up BioConductor on a computer that had
> never seen R before and did a clean install.  In all cases, I was unable
> to convert all probeids to nuIDs using lumiMouseV1.  My hope was that
> the new lumiMouseAll.db library would solve this problem.
> Bob 

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