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abnormal P-value from the "suppy.py diffSplice" #174

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gengbaobao opened this issue Oct 30, 2023 · 4 comments
Open

abnormal P-value from the "suppy.py diffSplice" #174

gengbaobao opened this issue Oct 30, 2023 · 4 comments

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@gengbaobao
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Hello developer,
There are too many equal p-value in the result of "suppy.py diffSplice".
My commond line is:
suppa.py diffSplice --method empirical -i all.ioi -p Ctrl_isoform.psi BM_isoform.psi -e Ctrl.tpm BM.tpm -pa -o Ctrl_BM_diffSplice_isoform
I also try to add the "-gc" parameter like this:
suppa.py diffSplice --method empirical -i all.ioi -p Ctrl_isoform.psi BM_isoform.psi -e Ctrl.tpm BM.tpm -gc -pa -o Ctrl_BM_diffSplice_isoform
Howerever, there are similar problems.

 Here is the part of my results:
Ctrl_isoform-BM_isoform_dPSI	Ctrl_isoform-BM_isoform_p-val

CALM2;PB.8231.1 -0.01657847 0.04995005
CALM2;PB.8231.2 0.01657847 0.04995005
CD40;PB.8726.1 -0.102306708 0.04995005
CENPQ;PB.11583.1 -0.188798533 0.04995005
CENPQ;PB.11583.2 0.188798533 0.04995005
COCH;PB.4633.2 -0.37545751 0.04995005
COCH;PB.4633.8 0.311427448 0.04995005
DENND2D;PB.1983.1 0.156882244 0.04995005
DENND2D;PB.1983.44 0.178530664 0.04995005
DVL3;PB.9764.11 0.310027991 0.04995005
ENSG00000259580_GPR176;PB.5281.1 -0.580624434 0.04995005
ENSG00000259580_GPR176;PB.5281.8 0.737802883 0.04995005
FEM1B;PB.5176.17 0.229988847 0.04995005
FOXJ3;PB.1836.17 -0.296775399 0.04995005
GAREM2;PB.7670.3 0.187286737 0.04995005
GSR;PB.13073.3 -0.04260686 0.04995005
HIVEP1;PB.11448.13 -0.320711264 0.04995005
INPP5F;PB.2609.6 -0.44106811 0.04995005
KIF23;PB.5179.8 -0.348268889 0.04995005
KREMEN2;PB.5497.9 0.534796343 0.04995005
LYRM1;PB.5546.1 -0.037861502 0.04995005
LYRM1;PB.5546.2 0.037861502 0.04995005
MED27;PB.13753.7 0.258339035 0.04995005
MRPL42P1;PB.10672.1 0 0.04995005
MRPS27;PB.11192.11 0.168481524 0.04995005
PER1;PB.6376.30 0.212415939 0.04995005
PLPBP;PB.12865.3 -0.120378402 0.04995005
RNGTT;PB.11962.49 0.291015043 0.04995005
RPS4Y1;PB.14205.1 0.065337043 0.04995005
RPS4Y1;PB.14205.2 -0.069529791 0.04995005
SEPHS1;PB.2662.9 -0.14339283 0.04995005
SLU7;PB.11374.2 -0.074892795 0.04995005
SPECC1;PB.6076.10 -0.332135461 0.04995005
SPECC1;PB.6076.4 0.375018165 0.04995005
TAB1;PB.9200.8 -0.301743279 0.04995005
TACC3;PB.10224.11 0.105345289 0.04995005
TACC3;PB.10224.16 0.095855675 0.04995005
TBC1D17;PB.7212.5 0.170028605 0.04995005
UBA7;PB.9918.20 0.216838746 0.04995005
UBE2Q1;PB.2083.1 0.045866321 0.04995005
UBE2Q1;PB.2083.2 -0.045866321 0.04995005
ZBTB8A;PB.1153.6 0.298387658 0.04995005
ZNF879;PB.11076.2 -0.366025273 0.04995005
ZNF879;PB.11076.3 0.33091838 0.04995005
novelGene_STX17-DT_AS;PB.13414.14 -0.316769584 0.04995005
novelGene_STX17-DT_AS;PB.13414.15 0.316769584 0.04995005

ASB2;PB.5011.4 -0.716067743 0.008991009
ASB2;PB.5011.5 0.65340794 0.008991009
ATP1A3;PB.7526.3 0.32396243 0.008991009
ATXN3;PB.5005.1 0.386166466 0.008991009
ATXN3;PB.5005.3 -0.425350996 0.008991009
BANP;PB.5725.2 -0.362833837 0.008991009
C2orf68;PB.8312.2 0.266074609 0.008991009
C2orf68;PB.8312.4 -0.348648988 0.008991009
CTNS;PB.6008.2 -0.500994813 0.008991009
DBN1;PB.11400.6 -0.383988536 0.008991009
EIF2B5;PB.9763.9 -0.386878081 0.008991009
ENSG00000276709;PB.520.1 -0.322588091 0.008991009
ENSG00000276709;PB.520.6 0.306779496 0.008991009
ENSG00000291107;PB.3645.16 0.751343657 0.008991009
ERN1;PB.6608.5 -0.37891646 0.008991009
ETV3;PB.2111.10 -0.826645556 0.008991009
GOLGA7;PB.12872.1 -0.195314364 0.008991009
KLHL9;PB.13559.1 0.481304201 0.008991009
LINC00494;PB.8733.1 -0.381428734 0.008991009
LOXL2;PB.13055.25 0.404944025 0.008991009
MFAP1;PB.5311.1 0.176710968 0.008991009
MRPL45;PB.541.1 0.190655631 0.008991009
MRPL45;PB.541.2 -0.206017351 0.008991009
MVP;PB.5580.16 0.28545561 0.008991009
NEIL1;PB.5196.1 -0.285418217 0.008991009
NEIL1;PB.5196.3 0.322617847 0.008991009
NSFL1C;PB.8783.2 0.238008452 0.008991009
NSFL1C;PB.8783.4 -0.339541597 0.008991009
PEX11A;PB.5441.1 0.373130644 0.008991009
PEX11A;PB.5441.2 -0.373130644 0.008991009
POU2AF2;PB.3195.4 -0.911281833 0.008991009
PRMT3;PB.2950.4 -0.379912011 0.008991009
@gengbaobao
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Is this result normal? If not, how can I modify it?

@EduEyras
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EduEyras commented Oct 30, 2023 via email

@gengbaobao
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Hello Eduardo,

Thanks for reply!
I check the PSI and TPM values and I don't see they have similar expression.
I'll show you three example of my data. Here are the part of PSI and TPM value (P-value=0.04, P-value=0.008 and P-value=0.001 respectively).

PSI:
#####################################################
Ctrl_isoform_1 Ctrl_isoform_2 Ctrl_isoform_3 Ctrl_isoform_4 Ctrl_isoform_5 BM_isoform_1 BM_isoform_2 BM_isoform_3 BM_isoform_4 BM_isoform_5

AARS1;PB.5932.16 0.002863842 0.0049032 0.008583554 0.006143318 0.006605211 0.036645015 0 0.086276155 0.050000889 0.024021956
ABR;PB.617.7 7.98E-11 0.081432394 0.207011154 0.13830743 0.000222683 0.000525855 4.19E-05 6.78E-06 0 3.23E-07
ACTN4;PB.7127.4 0.005885357 0.003393333 0.002725406 0.005792339 0.002854791 0.069903361 0.054260493 0.060069652 0.049217672 0.054136711
GDE1;PB.5823.5 0.20207694 0.247245794 0.229723244 0.311051469 0.313120707 0.278629716 0.121554352 0.122139276 0.252283414 0.262531896
ZC3H3_ENSG00000254859;PB.13228.6 0 0.039090326 0.026871015 0.047223116 0 0.33122771 0.005173215 0 0.507290171 0.324889072
##########################################
CALM3;PB.7178.7 0.406058563 0.525951733 0.52081499 0.517901032 0.496199163 0.364635068 0.358000665 0.360151941 0.366493088 0.423036544
DDX41;PB.11401.74 0.135791131 0.146336824 0.128767172 0.149961875 0.164338659 0.373038773 0.462321777 0.458728213 0.385126762 0.490239101
ECPAS;PB.13683.15 0.018186188 0.024270458 0.016910971 0.049231382 0.036925174 0.145282669 0.158230861 0.192435584 0.180978939 0.229359544
IDE;PB.2799.35 0.292701403 0.625782297 0.621281706 0.624102153 0.559220134 0.241342671 0.08335012 0.220997977 0.073749429 0.124704082
KLF13;PB.5069.2 0.198747089 0.021677736 0.353011394 0.158555359 0.163353262 0.438178873 0.317763493 0.570961542 0.259391999 0.524054826
PGS1;PB.6287.18 0.32611698 0.445098842 0.400899222 0.539605402 0.509913519 0.190354182 0.199610173 0.05599444 0.236577309 0.038528032
############################################
CD22;PB.7102.51 3.22E-09 5.26E-12 0.00037957 0.009141746 2.33E-05 0.006887264 0.001916509 0.085129446 0.008967055 0.043383391
DELE1;PB.10997.7 0.00028422 0.085656644 0.08958253 0.101872619 0.064394371 0.039332327 0 0 0 0
EDC4;PB.5661.27 0.101779013 0.067313493 0.259219111 0.109105265 0.109721763 0.010979881 3.65E-06 0.007054745 0.010312595 0.007705238
GPAT4;PB.12873.8 0.100850001 0.070029657 0.07242013 0.070213169 0.058659683 0.186067161 0.175556353 0.075251623 0.066576139 0.218900039
MST1R;PB.9919.3 0.374459075 0.547122666 0.144224446 0.405485724 0.404012725 0 0 0 0.116629007 0
###################################

Expression TPM
##############################################################
Ctrl01 Ctrl02 Ctrl03 Ctrl04 Ctrl05 BM01 BM02 BM03 BM04 BM05
PB.5932.16 0.569652 1.70179 2.30868 0.740823 2.05807 0.662671 0 0.872586 1.66225 0.625084
PB.617.7 1.66E-09 1.57174 3.8002 2.64483 0.00390669 0.00739502 0.000373013 0.000175222 0 3.76E-06
PB.7127.4 0.361797 0.328223 0.294353 0.541552 0.232015 2.55296 1.33969 3.51057 2.25583 2.20639
PB.5823.5 13.567 21.6608 18.3566 25.1618 21.4639 10.1235 3.35083 6.34766 8.03882 10.7505
#########################################################################
PB.7178.7 121.437 278.799 249.05 189.75 281.307 84.8008 59.6521 97.7909 64.4722 91.3981
PB.11401.74 7.93672 11.2319 8.54445 10.4256 11.0167 18.6134 16.2862 22.1152 15.1811 28.3195
PB.13683.15 0.826315 1.39055 0.890886 3.26921 2.19735 5.20271 4.98587 7.12919 5.36657 11.8975
PB.2799.35 12.8592 33.5532 25.813 43.708 28.7838 3.87582 1.18636 3.4887 1.26075 3.43793
PB.5069.2 19.2608 0.89468 46.4213 5.38387 11.734 23.316 6.1833 55.8103 5.07633 28.5588
PB.6287.18 9.80631 15.3027 14.2828 16.1415 16.2153 3.78655 1.91985 1.28331 3.53909 0.750231
############################################################################
PB.7102.51 1.69E-06 1.93E-09 0.0894076 1.71919 0.0071258 2.38976 0.476083 18.4437 4.53723 10.1792
PB.10997.7 0.0156471 4.75187 5.00593 4.58025 3.53815 1.96871 0 0 0 0
PB.5661.27 1.37712 1.93532 3.10209 2.29886 2.28326 0.208599 4.85E-05 0.15769 0.163485 0.185946
PB.12873.8 5.96435 4.69813 3.30181 3.25763 3.39846 8.59453 5.83417 3.86435 2.90588 10.0168
PB.9919.3 0.668331 2.08247 0.511025 3.11777 2.14966 0 0 0 0.0425264 0

@gengbaobao
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I also check the P-values and I find that these P-values is a Arithmetic sequence whose "common difference" is 0.00049901.

Example:

P-Value | common difference
0.04995005 |  
0.04945055 | 0.000499501
0.048951049 | 0.000499501
0.048451549 | 0.000499501
0.047952048 | 0.000499501
0.047452548 | 0.000499501
0.046953047 | 0.000499501
0.046453547 | 0.000499501
0.045954046 | 0.000499501
0.045454546 | 0.000499501
0.044955045 | 0.000499501
0.044455545 | 0.000499501
0.043956044 | 0.000499501
0.043456544 | 0.000499501
0.042957043 | 0.000499501
0.042457543 | 0.000499501
0.041958042 | 0.000499501
0.041458542 | 0.000499501
0.040959041 | 0.000499501
0.040459541 | 0.000499501
0.03996004 | 0.000499501
0.03946054 | 0.000499501
0.038961039 | 0.000499501
0.038461539 | 0.000499501
0.037962038 | 0.000499501
0.037462538 | 0.000499501
0.036963037 | 0.000499501
0.036463537 | 0.000499501
0.035964036 | 0.000499501
0.035464536 | 0.000499501
0.034965035 | 0.000499501
0.034465535 | 0.000499501
0.033966034 | 0.000499501
0.033466534 | 0.000499501
0.032967033 | 0.000499501
0.032467533 | 0.000499501
0.031968032 | 0.000499501
0.031468532 | 0.000499501
0.030969031 | 0.000499501
0.030469531 | 0.000499501
0.02997003 | 0.000499501
0.02947053 | 0.000499501
0.028971029 | 0.000499501
0.028471529 | 0.000499501

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@EduEyras @gengbaobao