Observations, Comments, and RFEs stemming from Pancan8 workshop
---------------------------------------------------------------
2012_10_24-

1)  Group each OV/BRCA/etc disease report by datatype, not analyses
    ACTION: GDAC Dev Meeting

2)  Put "nozzle-fied' sample table into top-level aggregate report, where
    each cell links to section of disease-specific report for that datatype, eg

										mirSeq		RPPA
	BLCA											408
	BRCA
	...
	GBM									 0
	...
	OV			...		...		...		454

	Here 408 links to BLCA_report.html#RPPA section
	Here 0 shows no link for GBM miRseq data ... ie no mirSeq pipelines run for GBM
	But	 454 links to OV_report.html::miRseq section, showing all available reports
	(and hence pipelines run) for OV::miRseq

    ACTION: GDAC Dev Meeting


3)  Why does PANCAN8 miR CNMF clustering show only 570 samples?  OV only????
	(looks suspiciously like only OV may have been taken, 491 GBM ignored?)

    ACTION: critical jira bug -- assign to Hailei

4)  Why no mirSeq clusters in PC8?
5)  or RPPA?

    ACTION: major jira bugs -- assign to Hailei

6)  IN OTHER WORDS:  PREPROCESS tasks NEED REPORTS, TO REFLECT FILTERING STEPS!

    ACTION: GDAC Dev Meeting

7)  Should we throw out correlations_by_gene (ie, by _<datatype>, in favor of by
    molecular subtype cluster?  (by-gene correlation essentially redundant: when
	a gene appears w/in in a subtype it naturally correlates same as subtype)

    ACTION: GDAC Dev Meeting

8)  Correlate vs. molecular subtypes (clusters) ... can table link to clusters,
    otherwise dificult to see what's meant visually  ... at present it links
	just to the cluster labels

    ACTION: GDAC Dev Meeting, low priority to discuss

9)  CopyNumber_CNMF appears in molecular_subtypes_VS_clinical 5 or 7 times!!!!
	(e.g. see BRCA, OV etc in  9/13 ...)

    *** Not present in 8/25 run ... crept in somewhere between 8/25 and 9/13 ...

    ACTION: critical jira bug -- assign to Will, include Hailei -- absolutely
		    must be fixed in current analysis run