Illumina probes not found message should be documented
|Illumina package v1.4
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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).
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