Illumina probes not found message should be documented

[Jari Häkkinen]

Extract information from below conversation and add it to the Illumina documentation.

I have recently installed the Illumina Plugins and have imported  
features for several Array Designs. We modified our config to  
generate the Bead Summary files and I have imported the data. Oddly  
have found that the Bead Summary files contain some rows with  
illumina codes that are not in the BGX files. For example the  
datasets from !HumanRef-8 arrays contain 324 probes that are not found  
in any of the various versions of BGX files are available from the  
Illumina web site. If I run these same datasets through !BeadStudio  
these these probes are not found in the !BeadStudio output.

Has anyone else run into this situation?

Yes, we have seen this also. Just select 'Probe not found=skip' when
importing the data to BASE and everything should work.

We experienced that as well. I believe that I have checked these probes 
and they were controls, so they can be ignored.

All of them are not necessarily controls since the number of probes 
missing in the bgx-files may change between Illumina revisions of 
bgx-files. Our interpretation is that some probes that used to be 
annotated with a gene has later been considered poor by Illumina (as we 
have only observed an increase in the number of unmatched probes for 
later bgx revisions).

Importantly, if you follow Nicklas's 'Probe not found=skip' 
recommendation, you will get the same number of probes (and the same 
probes) as when using !BeadStudio (!BeadStudio silently ignores the probes 
not in the bgx-files; you also end up with slightly different numbers of 
probes in !BeadStudio for different bgx revisions).

[Martin Svensson]

(In [1093]) References #182 The information is now inserted in the README file, in the section about Illumina Bead Summary (IBS) files.