modules detection

[maidach6]

hello, I am trying scGWAS on my plant scRNA data and after following the scGWAS Github repository i am not getting my significant modules in the top right side of the plot. I am new to this technique may be i am doing something wrong but i am unable to find its solution as my all cell type module plots having significant modules at different points on the plot. please help.

[bsml320]

can you please show me the figure?

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On Mon, May 12, 2025 at 6:19 PM maidach6 ***@***.***> wrote: *maidach6* created an issue (bsml320/scGWAS#2) <#2> hello, I am trying scGWAS on my plant scRNA data and after following the scGWAS Github repository i am not getting my significant modules in the top right side of the plot. I am new to this technique may be i am doing something wrong but i am unable to find its solution as my all cell type module plots having significant modules at different points on the plot. please help. — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACE2SKW3XTEBV36PHLFUY6L26BYRXAVCNFSM6AAAAAB45PUTK6VHI2DSMVQWIX3LMV43ASLTON2WKOZTGA2TMNBVGI4TANY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[maidach6]

This one is from my practice so far i have tried it on scRNA data from rice and plot the results with relaxed thresholds. I cannot understand why the significant modules did not appeared in the described area in scGWAS pipeline (upper right corner, above the dashed line).

[maidach6]

Please help!

[bsml320]

can you send me the raw data, e.g., the GWAS and scRNA-seq data. I can try on my side. The figure does not look right to me. The x-axis seems too large, from 0 to 15. We actually never saw such numbers. Both input data are normalized. The module scores should not spend such a wide range.

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On Thu, May 15, 2025 at 6:22 PM maidach6 ***@***.***> wrote: *maidach6* left a comment (bsml320/scGWAS#2) <#2 (comment)> Please help! — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACE2SKT5LOAAX7AMZHJ66KL26RTGJAVCNFSM6AAAAAB45PUTK6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQOBTGMYTQNBWGM> . You are receiving this because you commented.Message ID: ***@***.***>

[maidach6]

Yes, I can send. Thank you soo much for your response actually i am stuck at this for a long.

[maidach6]

Hello, With due respect!

I am sorry for taking a long to reply but i was trying again on my behalf to get better results. I have new result which i have attached below by the name "Rice_Root_Tip_scGWAS.png". I am attaching my expression matrix and the dataset which i used for Rice Root_tip scRNA-seq was derived from https://biobigdata.nju.edu.cn/scplantdb and the dataset which i had used is available with the ID: SRP309176 (Oryza sativa; Tissue: Root_tip).
The GWAS file which is used is taken from Huang Rice population.
Please help me to figure out this problem.

Thank you soo much!
Your kind response will be highly appreciated

MAF.Huang2015NC.Yield.2012SY.HeadingDate.zip

[bsml320]

The new result (Rice_Root_Tip_scGWAS.png <https://github.com/user-attachments/assets/76d047c9-a7d1-4021-a0b2-d3ccfa4f6fd1>) seems correct to me. Do you still need me to re-run the analyses?

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On Wed, May 21, 2025 at 3:52 PM maidach6 ***@***.***> wrote: *maidach6* left a comment (bsml320/scGWAS#2) <#2 (comment)> Hello, With due respect! I am sorry for taking a long to reply but i was trying again on my behalf to get better results. I have new result which i have attached below by the name "Rice_Root_Tip_scGWAS.png". I am attaching my expression matrix and the dataset which i used for Rice Root_tip scRNA-seq was derived from https://biobigdata.nju.edu.cn/scplantdb and the dataset which i had used is available with the ID: SRP309176 (Oryza sativa; Tissue: Root_tip). The GWAS file which is used is taken from Huang Rice population. Please help me to figure out this problem. Thank you soo much! Your kind response will be highly appreciated MAF.Huang2015NC.Yield.2012SY.HeadingDate.zip <https://github.com/user-attachments/files/20362549/MAF.Huang2015NC.Yield.2012SY.HeadingDate.zip> Rice_Root_Tip_scGWAS.png (view on web) <https://github.com/user-attachments/assets/76d047c9-a7d1-4021-a0b2-d3ccfa4f6fd1> — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACE2SKU3ES3GVAIOHW526ET27QWD7AVCNFSM6AAAAAB45PUTK6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQOJWHE3DAMRUGY> . You are receiving this because you commented.Message ID: ***@***.***>

[maidach6]

Yes please i want you to run for me just for once as i am a long list to perform the same thing so if i will face any issues in this run i can cope them at the intial steps.