Initial experimental branch.
Initial experimental branch.
Committing some uncommitted changes from October...
Merging mnf_funcs.c and list_test.c.
Removed support for 'RGList's, and for normalizing MM intensities.  Major refactoring of main functions; rewrote various parts with a functional approach.  Implemented summarization, as well as fold change and t-test analyses; consequently added support for identifying samples and replicates.
Added replicate variance to data frame returned by 'mnf'.
Added replicate variance to data frame in list returned by 'mnf'.
Removed some deprecated functions; increased verbosity.
Fixed three major bugs, rendering all previous versions unquestionably invalid.
Added two image functions to visualize inter-replicate variance and probe residuals on arrays; some minor refactoring and fixes; normalize.mnf now keeps dimnames(batch) intact.
Uhh...
Refactored image functions: mostly just added some options.
residuals.mnf.replicate no longer assumes sample IDs start at 1
Merge branch 'experimental' of binsrv2.iric.ca:~/workspace/rmnf into experimental
Bug fix: curly brace had been magically moved up by two lines...
Fixed typo and made a file path absolute.
Added R/nick_degs.R
Merge branch 'experimental' of ssh://pegpegpeg.dyndns.org:8787/home/serhalp/workspace/rmnf into experimental
Now actually computes ranks properly; can now also perform spatial normalization with multiple values for 'kb'.
Made hardcoded absolute path slightly less absolute.