Regarding pvalues in diffSplice

[heebaanjum]

Hi, I am running diffSplice for specific ioe files, with two developmental conditions in plants(Early reproductive stage and Middle Reproductive stage). The output file contains p_values either 0 or 1 (not ranging between 0 an 1). Could you please help me regarding this.

diffSplice command: python3 /home/uvr2/SUPPA/suppa.py diffSplice --method empirical --input MSU_v7_new_A3_strict.ioe --psi A3_Early.psi A3_Middle.psi --tpm TPM_Early TPM_Middle --area 1000 --lower-bound 0.05 -gc -pa -o A3_diffSplice Below is the screenshot of output A3_diffSplice.dpsi file .

Thank you for your help, Heeba

[EduEyras]

Thanks for your message

plotting the input values could help understand what is happening. E.g. you could plot the deltaPSIs as a function of average TPM, as described in the wiki page.

It could be that the A3 events don't much PSI variation, or very low associated TPM values.

Changing the parameter "Area" could help. But understanding the input data could be more useful to understand why this is happening

I hope this helps.

E

On Fri, 28 Oct 2022 at 22:01, Heeba Anjum @.***> wrote:

Hi, I am running diffSplice for specific ioe files, with two developmental conditions in plants(Early reproductive stage and Middle Reproductive stage). The output file contains p_values either 0 or 1 (not ranging between 0 an 1). Could you please help me regarding this.

diffSplice command: python3 /home/uvr2/SUPPA/suppa.py diffSplice --method empirical --input MSU_v7_new_A3_strict.ioe --psi A3_Early.psi A3_Middle.psi --tpm TPM_Early TPM_Middle --area 1000 --lower-bound 0.05 -gc -pa -o A3_diffSplice Below is the screenshot of output A3_diffSplice.dpsi file [image: Screenshot from 2022-10-28 16-27-12] https://user-images.githubusercontent.com/109336808/198571860-c4b315ae-e180-472b-b269-3943a563269a.png .

Thank you for your help, Heeba

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