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

[gengbaobao]

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]

Is this result normal? If not, how can I modify it?

[EduEyras]

Hi thanks for your email it could be that all these cases have similar PSI values in both conditions and the genes have similar expression, so they are tested within the same background distribution. It is not a problem in itself, it's a numerical coincidence. Please check the PSI values for those events. It could highlight the source of this. I hope this helps Eduardo

…

On Mon, 30 Oct 2023 at 23:11, gengbaobao ***@***.***> wrote: 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 — Reply to this email directly, view it on GitHub <#174>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB7C5BZUMQOMHNGSS3TYB6KQZAVCNFSM6AAAAAA6V5ABZOVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE3DQMRQGMZTCMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[gengbaobao]

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]

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