[BioC] Illumina Probe_ID used in the LIMMA package for neqc function

[William D'Avigdor]

Hi,

I am doing some Illumina analysis using HumanWG-6_V2 microarrays, and 
have been using the annotation file: HumanWG-6_V2_0_R4_11223189_A.bgx, 
and I am normalising using the NEQC function in the LIMMA package.

I know there are traditionally a number of Illumina identifiers and I am 
concerned that I may have potentially been using the wrong ones, and I'm 
not sure whether this has affected the normalisation proceedure, or 
anything at all.

After summarisation in Genome Studio, when looking at the 'Sample Probe 
Profile', the main identifiers that come up (and which I have used in 
LIMMA) are 'PROBE_ID' and 'SYMBOL', the first row being ILMN_1762337 and 
7A5 respectively. I also noticed that this PROBE_ID column was the one 
used in the Illumina example in the LIMMA manual.

HOWEVER, in Genome Studio, there is also a column called 'ProbeID'. This 
does not exist in the original annotation file 
(HumanWG-6_V2_0_R4_11223189_A), but it is identical to the 
Array_Address_ID (except for the preceeding 000s), the latter of which 
is both in Genome Strudio and in the Annotation file, and UNIQUE to the 
version of the microarray.

IN CONTRAST, in the 'Control Probe Profile' in Genome Studio, there is 
only the 'TargetID' and the 'ProbeID' available, the latter of which (I 
believe) is the Array_Address_ID?

HENCE, for the LIMMA input, I am wondering whether I am correct when I 
have included the Sample Probe ID text file (which includes PROBE_ID, 
that is, ILMN_1762337), and the Control Probe ID text file (which 
includes ProbeID instead, which is most likely the Array Address ID).

Many thanks in advance,
William d'Avigdor