On Mon, Dec 1, 2008 at 4:39 AM, Renaud Gaujoux <
renaud@mancala.cbio.uct.ac.za> wrote:

> Hi Pan,
>
> thanks for your answer. I've been (and still am) struggling a bit to get
> consistent and up to date annotation for my data.
>
> So, I guess it is more reliable to use the lumiHumanAll.db package?
>
> However, what about the probes that are note annotated in lumiHumanAll but
> look like interesting for my study (i.e. appearing in my top lists for
> differential expression or classification power).
> I've got such probes that are annotated neither packages lumiHumanAll.db
> nor in lumiHumanV2 but are in illuminaHumanv2.
>
> Hence no package give me consistent annotation for my top genes. However
> I've got an annotation file (that came with the array data, I guess output
> by BeadStudio) that gives me annotations for all of my probes. But as you
> mentioned, these might be outdated, which actually bothers me. Any
> suggestion about that?
>
> By the way, how come that even Illumina "proprietary" packages
> (illuminaHumanv2.db) don't annotate correctly their own probes? :(
>
> Thanks again for your help and clarification, and the lumi package.
>

Hi, Renaud.  When in doubt, it is a good idea to do your own blasting of the
probe sequences for those probes that look interesting.  Assuming that you
are going to do that with only a few probes, it is pretty straightforward to
do that on the NCBI website to get answers.  My guess is that you might see
a confusing picture for probes that have differing annotations over time, so
it will be up to you to determine what to do with such probes.  Sometimes, a
second assay such as PCR will be necessary to help flesh out what a probe is
actually measuring.

Sean



>
>
> Pan Du wrote:
>
>> Hi Renaud,
>>
>> The reason of discrepancy is due to the different mapping criteria. Both
>> "lumiHumanAll.db" and "illuminaHumanv2.db" libraries are based on Blasting
>> result of RefSeq database. The "lumiHumanAll.db" library is nuID indexed
>> and
>> includes all the probes of different versions. For the mapping from probe
>> to
>> RefSeq, it defined both sensitivity and specificity (see the vignette
>> "IlluminaAnnotation.Rnw" in the lumi package). As a result, it might
>> include
>> less mapping than "illuminaHumanv2.db" because "lumiHumanAll.db" filtered
>> out some dubious mappings (e.g., one probe has multiple perfect mapping.)
>>
>> The "lumiHumanV2" library was built based on the original annotation by
>> Illumina company. As a result, it has much more probe mappings. However,
>> many mappings might be outdated because of the updates of the genome
>> annotation.
>>
>> Hope this will clarify the confusion.
>>
>>
>> Pan
>>
>>
>> On 11/28/08 5:00 AM, "bioconductor-request@stat.math.ethz.ch"
>> <bioconductor-request@stat.math.ethz.ch> wrote:
>>
>>
>>
>>> Date: Thu, 27 Nov 2008 16:03:36 +0200
>>> From: Renaud Gaujoux <renaud@mancala.cbio.uct.ac.za>
>>> Subject: [BioC] Illumina annotation packages discrepancy
>>> To: bioconductor@stat.math.ethz.ch
>>> Message-ID: <492EA8B8.5000400@cbio.uct.ac.za>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>
>>> Hi list,
>>>
>>> I've got BeadSummary data from Illumina (Array content:
>>> HUMANREF-8_V2_11223162_B.XML.xml).
>>> I imported it in R using the function lumi.batch.
>>> This automatically computed the nuID for each probe and set the
>>> annotation package to lumiHumanAll.db.
>>> This is all good.
>>>
>>> BUT, when I do
>>>
>>> lookUp(nuIDs, 'lumiHumanAll.db', 'GENENAME')
>>>
>>> I get 2921out of 20589 probes with NA.
>>>
>>> If I do the same using the old annotation package lumiHumanV2:
>>>
>>> lookUp(nuIDs, 'lumiHumanV2', 'GENENAME')
>>>
>>> I get 454 out of 20589 probes with NA.
>>>
>>> Finally, if I do the same using the annotation package
>>> illuminaHumanv2.db (but based on the corresponding TargetIDs):
>>>
>>> lookUp(targetIDs, 'illuminaHumanv2.db', 'GENENAME')
>>>
>>> I get 2041out of 20589 probes with NA.
>>>
>>> Can anybody give me an explanation for that discrepancy? And what
>>> annotation package I should use as it looks like some interesting probes
>>> (for my experiment) don't have annotation in the new version?
>>>
>>> Also I could not find any reference to that HUMANREF-8_V2_11223162_B
>>> annotation (neither on Illumina website nor in Bioconductor packages). I
>>> only found information about HUMANREF-8_V2_11223162_A. Is the letter
>>> suffix (A or B) really important?
>>>
>>> Thanks
>>>
>>>
>>>
>>>
>>
>>
>> ------------------------------------------------------
>> Pan Du, PhD
>> Research Assistant Professor
>> Northwestern University Biomedical Informatics Center
>> 750 N. Lake Shore Drive, 11-176
>> Chicago, IL  60611
>> Office (312) 503-2360; Fax: (312) 503-5388
>> dupan (at) northwestern.edu
>> ------------------------------------------------------
>>
>>
>>
>>
>>
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