Mouse-Imaging-Centre
mincFDR - method "qvalue", "pFDR: and "fastqvalue" are broken-ish
The qvalue package has been removed from CRAN, and can not be installed anymore through install.packages("qvalue"). This currently breaks the above mentioned methods for mincFDR. Also, when mincFDR is called using a .mincSingleDim the df and statType arguments are not properly parsed/used. In the main mincFDR function they are overwritten right away by looking at the attributes "df" and "stat-type". If these are not present in the minc file object, mincFDR will fail.
The first half of this has been fixed, our package description now adds bioconductor as an extra repository, bioconductor has up-to-date versions of qvalue. For the second part, I'm not sure if the code has changed since you raised the issue, but it seems mincFDR.mincMultidim ignores stat-type and df, not just mincFDR.singleDim.
Before I fix this, any ideas on the priority we should give each condition? My inclination is argument > attribute, but perhaps the converse if the only use case for the arguments is when the attributes weren't set properly somehow.
