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reneshbedre / bioinfokit

Bioinformatics data analysis and visualization toolkit
MIT License
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Volcano plot - AssertionError: either significant or non-significant genes are missing; try to change lfc_thr or pv_thr to include both significant and non-significant genes #22

Closed tomasflyo closed 3 years ago

tomasflyo commented 3 years ago

Hi,

The library is installed correctly and the command works with no problem on the example data, but when I am running the library on my data I get the following error: >>>visuz.gene_exp.volcano(df=df, lfc='Fold_change', pv='p_value', show=True) AssertionError: either significant or non-significant genes are missing; try to change lfc_thr or pv_thr to include both significant and non-significant genes I tried playing with the thresholds and excluding columns/rows with NaN values. Nothing helped.

Any advice?

reneshbedre commented 3 years ago

@tomasflyo

To visualize the volcano plot better, visuz.gene_exp.volcano assumes that you have up, down and normal (that does not meet threshold criteria for up and down) regulated genes. In your dataset, one or more of those categories are missing and hence you are getting an error. Can you please share your dataset with me on reneshbe@gmail.com? I will help you figure it out.

tomasflyo commented 3 years ago

Hi Renesh, Thanks! Sent

On Tue, Jan 26, 2021, 17:12 Renesh Bedre notifications@github.com wrote:

@tomasflyo https://github.com/tomasflyo

To visualize the volcano plot better, visuz.gene_exp.volcano assumes that you have up, down and normal (that does not meet threshold criteria for up and down) regulated genes. In your dataset, one or more of those categories are missing and hence you are getting an error. Can you please share your dataset with me on reneshbe@gmail.com? I will help you figure it out.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/reneshbedre/bioinfokit/issues/22#issuecomment-767609288, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALDKA4XHI7ZSVJX56YHGJEDS33LV7ANCNFSM4WTHZXTA .

aknour commented 3 years ago

Hey Renesh,

I'm having the same issues as @tomasflyo, would you mind if I sent my data to you as well? Thanks!

Best, Ahmed

reneshbedre commented 3 years ago

@aknour

Yes, you can send it.

aknour commented 3 years ago

Hey Renesh,

Thank you for getting back to me! I'm trying to create a volcano plot on jupyterlab using your tutorial, but I'm getting this error: "AssertionError: either significant or non-significant genes are missing; try to change lfc_thr or pv_thr to include both significant and non-significant genes" Here is the dataset I'm using: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111345. I altered the original data by normalizing, transforming and concatenating categorical values to fit the format of your tutorial. I believe the issue may be in the way I calculated the p-value. If so, would you suggest any way to effectively calculate the p-values for the two columns?

Best, Ahmed [image: Screen Shot 2021-04-27 at 5.06.57 PM.png] [image: Screen Shot 2021-04-27 at 5.07.33 PM.png]

On Fri, Apr 23, 2021 at 2:58 PM Renesh Bedre @.***> wrote:

@aknour https://github.com/aknour

Yes, you can send it.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/reneshbedre/bioinfokit/issues/22#issuecomment-825945662, or unsubscribe https://github.com/notifications/unsubscribe-auth/APIGRSAXO7GYRX33RECL73TTKHUQJANCNFSM4WTHZXTA .

--

Ahmed Nour

University of California, Berkeley

B.A. Molecular and Cell Biology

@.*** | (510)205-2443

mmartino1440 commented 1 year ago

@reneshbedre can I send you my data for some assistance with the same issue @tomasflyo had?