Hello, I had a problem with mas5calls (see below). I am working with a YG_S98 array and I have seen in the archives this problem arose a few months ago. So I'd be surprised it has not been fixed. (I installed all the default Bioconductor packages today) 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? Many thanks in advance for your help and support, Emmanuel > 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

Hi Emmanuel, Emmanuel Levy <emmanuel.levy@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

Hello, I have a problem with mas5calls, I got the following error message: > 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 I tried 2 versions of the affy package: Package: affy Version: 1.6.6 Date: 2005-04-25 And the regular one Package: affy Version: 1.5.8-1 Date: 2004-10-20 I am working with a YG_S98 array and I have seen in the archives that this problem arose a few months ago. As far as I understood the problem was due to oligo sets of size 1 but I thought it had been corrected. Any idea is very welcome! Many thanks in advance, Emmanuel