p-value of 0 output rMATS

[Wan Fahmi]

Hello

I am just wondering whether why the p-value=0 from the output of rMATS SE.MATS.JunctionCountOnly.txt. As the results is sorted by p-value, does it mean the highest gene is the most significant splice variant between 2 samples? I have got at least 92 genes with p-value=0.

And one more question why does IJC_SAMPLE_2 (TPM1) has a value of

1,355,248,775,685 even though it only has 3 replicates.

ID	GeneID	geneSymbol	chr	strand	exonStart_0base	exonEnd	upstreamES	upstreamEE	downstreamES	downstreamEE	ID	IJC_SAMPLE_1	SJC_SAMPLE_1	IJC_SAMPLE_2	SJC_SAMPLE_2	IncFormLen	SkipFormLen	PValue	FDR	IncLevel1	IncLevel2	IncLevelDifference
10208	ENSG00000140416	TPM1	15	+	63353911	63353987	63353396	63353472	63354413	63354476	10208	94,120,83	21,19,24	1,355,248,775,685	64,12,42	175	100	0	0	0.719,0.783,0.664	0.992,0.996,0.987	-0.27
10280	ENSG00000082397	EPB41L3	18	-	5398019	5398142	5397391	5397425	5406775	5406967	10280	134,284,127	18,55,61	0,0,2	11,16,8	199	100	0	0	0.789,0.722,0.511	0.0,0.0,0.112	0.637
12537	ENSG00000138162	TACC2	10	+	123989865	1.24E+08	1.24E+08	1.24E+08	1.24E+08	1.24E+08	12537	0,0,1	5,26,11	176,219,182	2,2,3	189	100	0	0	0.0,0.0,0.046	0.979,0.983,0.97	-0.962
13432	ENSG00000131018	SYNE1	6	-	152451854	1.52E+08	1.52E+08	1.52E+08	1.52E+08	1.52E+08	13432	36,17,39	23,20,28	68,74,121	2,0,2	158	100	0	0	0.498,0.35,0.469	0.956,1.0,0.975	-0.538
13575	ENSG00000172915	NBEA	13	+	36220005	36220068	36202217	36202385	36220395	36220485	13575	0,0,0	53,30,25	12,11,13	2,1,0	162	100	0	0	0.0,0.0,0.0	0.787,0.872,1.0	-0.886
13581	ENSG00000064042	LIMCH1	4	+	41689856	41689934	41687726	41687847	41691543	41691652	13581	43,84,34	32,69,87	177,102,92	38,16,34	177	100	0	0	0.432,0.408,0.181	0.725,0.783,0.605	-0.364
1373	ENSG00000079819	EPB41L2	6	-	131201283	1.31E+08	1.31E+08	1.31E+08	1.31E+08	1.31E+08	1373	5,4,2	11,31,67	36,48,26	0,0,2	162	100	0	0	0.219,0.074,0.018	1.0,1.0,0.889	-0.859
13992	ENSG00000132305	IMMT	2	-	86397871	86397964	86393630	86393767	86398330	86398435	13992	48,86,78	0,0,0	8,19,44	161,114,130	192	100	0	0	1.0,1.0,1.0	0.025,0.08,0.15	0.915
14135	ENSG00000182287	AP1S2	X	-	15858619	15858714	15845014	15845495	15863501	15863639	14135	3,1,0	37,51,73	254,50,113	54,29,41	194	100	0	0	0.04,0.01,0.0	0.708,0.471,0.587	-0.572
1522	ENSG00000058404	CAMK2B	7	-	44279187	44279262	44274237	44274275	44280305	44280348	1522	214,362,126	7,15,7	4,0,0	72,67,94	174	100	0	0	0.946,0.933,0.912	0.031,0.0,0.0	0.92
15382	ENSG00000154556	SORBS2	4	-	186598150	1.87E+08	1.87E+08	1.87E+08	1.87E+08	1.87E+08	15382	1,0,5	32,43,16	1,026,286,286	196,64,100	199	100	0	0	0.015,0.0,0.136	0.725,0.692,0.59	-0.619
16332	ENSG00000117114	LPHN2	1	+	82452584	82452713	82450942	82451039	82456074	82457052	16332	65,48,11	1,3,3	0,0,0	24,36,41	199	100	0	0	0.97,0.889,0.648	0.0,0.0,0.0	0.836
1718	ENSG00000022267	FHL1	X	+	135291401	1.35E+08	1.35E+08	1.35E+08	1.35E+08	1.35E+08	1718	71,114,141	68,151,271	73,11,15	2,254,490,683	199	100	0	0	0.344,0.275,0.207	0.016,0.011,0.011	0.263
17298	ENSG00000152620	NADKD1	5	-	36208726	36208792	36207271	36207367	36211945	36212024	17298	3,3,18	47,49,55	40,22,14	12,6,6	165	100	0	0	0.037,0.036,0.166	0.669,0.69,0.586	-0.569
17516	ENSG00000145362	ANK2	4	+	114299245	1.14E+08	1.14E+08	1.14E+08	1.14E+08	1.14E+08	17516	0,0,0	18,61,29	29,67,52	32,29,37	191	100	0	0	0.0,0.0,0.0	0.322,0.547,0.424	-0.431
17521	ENSG00000145362	ANK2	4	+	114244914	1.14E+08	1.14E+08	1.14E+08	1.14E+08	1.14E+08	17521	16,22,33	138,143,113	52,77,112	6,12,23	135	100	0	0	0.079,0.102,0.178	0.865,0.826,0.783	-0.705
17523	ENSG00000145362	ANK2	4	+	114293688	1.14E+08	1.14E+08	1.14E+08	1.14E+08	1.14E+08	17523	54,47,25	255,232,163	98,153,184	5,6,7	192	100	0	0	0.099,0.095,0.074	0.911,0.93,0.932	-0.835
18138	ENSG00000099204	ABLIM1	10	-	116213137	1.16E+08	1.16E+08	1.16E+08	1.16E+08	1.16E+08	18138	46,105,74	19,21,60	313,261,263	33,39,14	199	100	0	0	0.549,0.715,0.383	0.827,0.771,0.904	-0.285
19138	ENSG00000138326	RPS24	10	+	79797722	79797740	79796951	79797062	79799961	79799982	19138	40,92,32	5,617,241,211	356,255,223	382,290,210	117	100	0	0	0.057,0.098,0.022	0.443,0.429,0.476	-0.39

[Juw Won Park]

Hello,

Zero P-value and FDR are generated when the actual value is smaller than the numerical accuracy cutoff, which is usually 2.2e-16. Therefore, zero P-values can be interpreted as P<= 2.2e-16.

For the number of replicates, please check that what was the data type you used for the column when you imported the data to your spreadsheet. Make sure to use 'text' for this column. If "general" was used, the excel often interprets it as numbers and put extra commas automatically.

Thanks,

Juw Won

[Xiao Lei]

Hi, Juw Won,

I have the same problem even when I imported the rMATS text output (e.g. SE.MATS.JC) to Excel as "text" as you suggested, I have three samples but in IJC_SAMPLE_1 I see (497,051,365,640). As you said, excel interprets it as numbers and puts extra commas automatically.  Excel sucks.

Thanks,

Xiao