Draft Analysis Run Notes

For each data run a new panel should be added here, describing the significant functional or data changes in that analysis run. Mike will cut them from here and paste to the public page upon releasing that run

If sparse, do diffs with last analysis run, to see new tasks/data added (and optionally ask team, via email, to verify). The /wiki/spaces/GDAC/pages/844334194

Spring 2016 Analysis Run

This is likely to be either the penultimate or perhaps even final standard Firehose analysis run of the TCGA project. Custom AWG runs will continue for TCGA as needed.
Summary of sample changes (see the comprehensive samples report for more details):
BCR
+1
(11368 total)
Clinical
+32
(11196 total)
CN
+2
(10987 total)
MAF
+313
(7099 total)
Methylation
+1
(10972 total)
miRSeq
+2
(10156 total)
mRNASeq
+164
(10267 total)
rawMAF
+2072
(6322 total)
RPPA
+627
(7429 total)
APOBEC pipelines updated:
1. used median filtering in primary APOBEC analysis
2. in downstream clinical correlations, corrected names of categorical variables and descriptions of how they were utilized
cNMF clustering improvement: new criteria used to select best cluster, identical to that describe in Summer 2014 run (see below) for consensus hierarchical clustering:
The cophenetic correlation coefficients and average silhouette values are used to determine the k with the most robust clusterings. From the plot of cophenetic correlation versus k, we select modes and the point preceding the greatest decrease in cophenetic correlation coefficient, and from these choose the k with the highest average silhouette value.
Survival analysis: for all clinical correlations
1. Modified the p-value calculation of survival analysis with continuous data. It now uses the quantile interval categorical values instead of continuous values.
2. Previously it had one hazard ratio value for one continuous value, but now has multiple hazard ratio values for quantile interval curves (and are now reflected in the plot legends)
FireBrowse:
1. updated to reflect these run results
2. iCoMut:
  1. loaded 4 additional disease cohorts: DLBC, ESCA, SARC, and THYM
  2. Completed most of work for major new release, stay tuned for announcement next week, incorporating many graphical and data exploration enhancements

Tasks Under Development

Migrated implementation of our clustering codes away from GenePattern into FH native jobs, consolidating and simplifying along the way (needs more description/tailoring)
The spearman correlation was used in the pipeline of Correlate_mRNAseq_vs_Mutation_APOBEC.

Table from 2013_09_23 analysis run; keep until next run is posted which corrects the GAF 3.0 issues

THCA				SKCM				LGG				KIRP
	GAF 2.1 323 Samples 6806 Mutations	GAF 3.0 401 Samples 6736 Mutations			GAF 2.1 228 Samples 189759 Mutations	GAF 3.0 228 Samples 189948 Mutations			GAF 2.1 217 Samples 25172 Mutations	GAF 3.0 220 Samples 23947 Mutations			GAF 2.1 111 Samples 7907 Mutations	GAF 3.0 112 Samples 7367 Mutations
Rank	Gene		2.1 Rank	Rank	Gene		2.1 Rank	Rank	Gene		2.1 Rank	Rank	Gene		2.1 Rank
1	NRAS	NRAS	1	1	C15orf23	C15orf23	1	1	IL32	TEAD3	5275	1	IL32	KCNK5	354
2	BRAF	BRAF	2	2	CDKN2A	POLDIP2	6212	2	IDH2	IL32	1	2	CDC27	CDC27	2
3	HRAS	HRAS	3	3	NRAS	NUDT11	16950	3	IDH1	ATRX	5	3	NF2	IL32	1
4	EMG1	OTUD4	793	4	BRAF	CDKN2A	2	4	TP53	PRCP	950	4	PPARGC1B	NF2	3
5	PTTG1IP	EIF1AX	14	5	OXA1L	NRAS	3	5	ATRX	IDH2	2	5	SFRS2IP	PPARGC1B	4
6	RPTN	NUP93	500	6	TP53	BRAF	4	6	CIC	IDH1	3	6	MET	PCDHGC5	12984
7	TG	NLRP6	26	7	STK19	OXA1L	5	7	FUBP1	TP53	4	7	ELF3	MET	6
8	TMCO2	PPM1D	13	8	PTEN	TTN	18	8	NOTCH1	HEATR3	239	8	PCF11	PLAC4	36
9	R3HDM2	MUC7	17	9	DSG1	UGT2B15	17	9	PIK3R1	CIC	6	9	LGI4	PCF11	8
10	PRB2	OR56A1	43	10	PPP6C	TP53	6	10	PIK3CA	FUBP1	7	10	RAB27B	LGI4	9

BCR	+1	(11368 total)
Clinical	+32	(11196 total)
CN	+2	(10987 total)
MAF	+313	(7099 total)
Methylation	+1	(10972 total)
miRSeq	+2	(10156 total)
mRNASeq	+164	(10267 total)
rawMAF	+2072	(6322 total)
RPPA	+627	(7429 total)