[BioC] siggenes error with rma & wilcoxon test

Ken Termiso jerk_alert at hotmail.com
Fri Oct 14 19:04:32 CEST 2005

Hi all,

I was pretty sure this was already out there on the mailing list, but i 
can't seem to find the post..

I get a reproducible error when calling sam() from siggenes (latest siggenes 
v1.2.17) with RMA-normalized data. It throws the error on 133aV2 chips with 
only 2 reps (not with 3) and with hu95 chips with 3 replicates.

The error msg is:

>Error in "names<-.default('*tmp*', value = c("100_g_at", "1000_at", 
>"1001_at", : 'names' attribute [12625] must be the same length as the 
>vector [12551]

I haven't dug thru the siggenes code yet b/c I think this error has been 
discussed here - doesn't this happen when multiple replicate samples have 
identical expression values (which can happen with RMA, due to the median 
polish) ?  Then with SAM, using Wilcoxon you get some probes with identical 
ranks and when the ranks are sorted, some are equal so they drop out, but 
the names vector is still the same length, so it crashes...?

Just wondering if that's what is happening...

Thanks for any help,

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