[BioC] Problem reading ArrayVision files

[Gordon Smyth]

Dear Michael,

I have fixed read.maimages() in limma 2.9.17 so that it reads Array 
Vision files again correctly.

Note however that the problem you observed previously with "printer 
layout information does not match M row dimension" is a different 
problem. This is caused by the fact that your GAL file has more rows 
than your data files. The problem is that spots corresponding to 
"empty", "EMPTY", "buffer" etc spots have been removed from the data files.

Unless you can figure out how to match up the rows of your GAL file 
with the rows of your data files, you can't use readGAL() and 
therefore can't use print-tip-loess normalization in limma. You can 
still use ordinary "loess" normalization.

Best wishes
Gordon