illuminaHumanv4.db - PROBEQUALITY - Meanings of the asterisks

Question

[Tobias.Wohland]

Hi @ all,

can anyone tell me or maybe describe the meaning of those asterisks which are used in the illuminaHumanv4.db Bioconductor-Package? They recommend to use only a match if the quality is good or perfect but there are also the categories good***, perfect*** and perfect****! I found some questions within the internet regarding this question but obviously no one has an answer. Does someone here has an idea?

Thanks in advance.

Best,
Tobi

Answer 1

[Tobias.Wohland]

Hi @ all,

Because it seems that no one has an appropriate answer to my question I asked one of the authors of the package for a description. Here is his answer:

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**** - the probe maps to a transcript in one of the databases in the manner specified (either "good" or "perfect"), but the transcript itself does not seem to map well to the genome. Whether it is an error in the transcript database, a failing of the reference genome, or the product of some post-transcriptional modification has to be assessed on a case by case basis

*** - the probe maps to a transcript in one of the databases in the manner specified (either "good" or "perfect") but the coding zones of that transcript are not annotated.

I can't remember which, off the top of my head, but I think that one of these classes generically has poor signal and so may 'dilute' any FDR control.

I certainly wouldn't want to ignore them, but if one of them comes up at the top of a gene-list you may want to give some attention to whether the annotation is believable for that probe.

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Many thanks to the authors of the package who gave me a very fast and satisfying answer. It will be also added to the documentation of the package in the near future. Hopefully this will help people who have the same question.

Best,
Tobi