Big cleanup of affymatrix importer. Now use E@exprs to get matrix from loaded data.

Also made row and colname import better by ensuring vector-handling, ensuring that getting single column/row data works without being converted into a single string instead of string in a list.
Removed ;1-hack and use NO_CONVERSION to ensure no extra computation is done when calculating r stuff.
Now AffyMatrix data is named as such.

workflows/go_workflow.py

@@ -186,19 +186,25 @@ class CelFileImportFunction(Function):
         chooser.add_filter(cel_filter)
         chooser.add_filter(all_filter)
 
+        try:
             if chooser.run() == gtk.RESPONSE_OK:
-            logger.log('debug', "Selected files: %s" % ", ".join(chooser.get_filenames()))
                 rpy.r.library("affy")
-            # hack: we append ";1" to make sure no r-object is returned to python (faster)
-            rpy.r('At.aBatch <- ReadAffy(filenames=c("%s"));1' % '", "'.join(chooser.get_filenames()))
-            # we destroy it immediately to keep it from being on
-            # screen while we do something with the files
-            chooser.destroy()
-            # also here we append ";1"
-            rpy.r('At.eSet <- expresso(At.aBatch, bg.correct=F, summary.method="liwong", pmcorrect.method="pmonly", normalize.method="qspline");1')
-            m = rpy.r('At.m <- exprs(At.eSet)')
-            rownames = rpy.r('rownames(At.m)') 
-            colnames = rpy.r('colnames(At.m)') 
-            return [dataset.Dataset(m, (('ids', rownames), ('filename', colnames)))] 
+    
+                silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
+                silent_eval('E <- ReadAffy(filenames=c("%s"))' % '", "'.join(chooser.get_filenames()))
+
+                m = rpy.r('m <- E@exprs')
+    
+                vector_eval = rpy.with_mode(rpy.VECTOR_CONVERSION, rpy.r)
+                rownames = vector_eval('rownames(m)') 
+                colnames = vector_eval('colnames(m)') 
+
+                # We should be nice and clean up after ourselves
+                rpy.r.rm(["E", "m"])
+                
+                if m:
+                    return [dataset.Dataset(m, (('ids', rownames), ('filename', colnames)), "AffyMatrix Data")] 
                 else:
+                    logger.log("notice", "No data loaded from importer.")
+        finally:
             chooser.destroy()