[Bioc-devel] Bioc-devel Digest, Vol 40, Issue 3

bmb at bmbolstad.com bmb at bmbolstad.com
Fri Jul 13 01:47:31 CEST 2007

Note that the current C code does appropriately handle ties (depending on
your definition of appropriate) and has done so for a long time (over 5

Cut from code comment:

" ** Apr 19, 2002 - Update to deal more correctly with ties (equal rank)"



>>Hi Seth & Ben,
>>thanks for your clarifying comments!
>> > [moved to bioc-devel, where this should have started I think]
>>Sorry if I have been stepping on feet... the reason for posting to the
>>bioc user list was that more than once I have (sadly) seen people
>>looking at histogrammes such as that of qx shown in my previous post,
>>and using the suggested "cutoff" e.g. to discriminate between expressed
>>and un-expressed genes, and the like. I hope that this does not sound to
>>presumptuous, but I think it is a good thing to educate users to
>>critically assess such results.
>>Btw, normalizeQuantiles from the limma package appears to deal with NA
>>values more gracefully (but it is written in R, hence slower). I think
>>it assumes that the missingness mechanism is random.
> Yes it does.
> The reason the R version is a bit slower than C is mainly because of
> the need to handle NAs and to treat ties carefully. Without these
> considerations, the R implementation is nearly as fast. Try
> normalizeQuantiles(ties=FALSE) for more speed.
> Regards
> Gordon
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