[BioC] mas5calls stops with an error

[Seth Falcon]

Hi Emmanuel,

Emmanuel Levy <emmanuel.levy at gmail.com> writes:
>> data.call = mas5calls(data.raw)
>> Getting probe level data...
>> Computing p-values
>> Making P/M/A Calls
>> Error in if (y < alpha1) { : missing value where TRUE/FALSE needed

What version of R did you see this with?  I'm wondering if you have a
mismatch using Bioconductor 1.5 with the recently released R 2.1.0
(not compatible).

> If the solution is to download the "in developement" affy package,
> then I would have another question: I tried that and installed it in a
> different directory. Now, the problem is I can't load it. I added the
> path in R_LIB, but I guess by default R looks first in
> /usr/lib/R/library/ and loads the "old" affy package first. Would it
> be possible to change that?

I'm assuming you are running R on a unix-like system.  The R_LIBS
environment variable is like PATH in that it can contain a list of
package library directories separated by ":".  The default R system
package library is alwasy appended (not prepended) to the search path.

So when you add the new directory to R_LIBS (not R_LIB), the order
matters as R will search for packages in the order listed.

Hope that helps some.

+ seth