[BioC] siggenes error with rma & wilcoxon test
jerk_alert at hotmail.com
Fri Oct 14 19:04:32 CEST 2005
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  must be the same length as the
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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