[BioC] Problem with limma topTable

Gordon K Smyth smyth at wehi.EDU.AU
Sun Nov 9 22:58:03 CET 2008

Dear Zhuoxun Chen,

Thanks for the bug report.  Now fixed in R 2.16.3.

Best wishes

-------- original message ----------
[BioC] Problem with limma topTable
Chen, Zhuoxun Zhuoxun_Chen at URMC.Rochester.edu
Sat Nov 8 01:01:33 CET 2008

Dear Bioconductors,

I came across the following problem after I switched my work to another 
computer, install the R 2.8.0. The same code works fine in my old computer 
with R 2.7.2. I would like to ask for your help.


If I type in:
   TB <- topTable(fit3, coef=1, p=0.05, lfc=2, n=1000, adjust="BH")
I will get an error
   Error in M[sig, ] : incorrect number of dimensions

However, if I change the command to
   TB <- topTable(fit3, coef=1, p=1, lfc=0, n=1000, adjust="BH")
It works fine.
So, it seems like the error comes up whenever I need to cutoff some of the 

Here is my sessionInfo:
R version 2.8.0 (2008-10-20)

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] statmod_1.3.6   vsn_3.8.0       affy_1.20.0     Biobase_2.2.0
[5] lattice_0.17-15 limma_2.16.2

loaded via a namespace (and not attached):
[1] affyio_1.10.1        grid_2.8.0           preprocessCore_1.4.0

Thank you very much!

Zhuoxun Chen

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