
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.

Problem:

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 probes.

Here is my sessionInfo:
R version 2.8.0 (2008-10-20) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=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

	[[alternative HTML version deleted]]

