P less than 5e-8 but it says doesnt' exist about focus

[sookwah-yee]

Hi, I also have the same issues that I have empty log file say that there is not p<5e-8. Not sure if anyone response to @Captain-Pam ? Was this issue resolve?

[Captain-Pam]

Hi, I also have the same issues that I have empty log file say that there is not p<5e-8. Not sure if anyone response to @Captain-Pam ? Was this issue resolve?

There has been no solution to this problem. If you are interested, can we try to solve it together?

[sookwah-yee]

I am interested to work together. I also have empty log file. I notice that the p<5e-8 is a warning and wasn't an error. I also tried using lower threshold and does not work. It is frustrating and I cannot move forward using it. I also email the creator, but has not heard back from him.

[sookwah-yee]

Hi @Captain-Pam, I think I may have a reason. I need to use the focus.db rather than gtex_v7.db https://www.dropbox.com/s/ep3dzlqnp7p8e5j/focus.db?dl=0
Try and see if it works for you after switching to focus.db. It is working for me now. I am not sure why gtex_v7.db not working for me.

[quattro]

Apologies for delayed response. Seeing this thread now. A few things:

1. I plan to replace the v7 db with an updated v8 soon.
2. Can you manually output regions that contain p < 5e-8 and contrast those with the pre-defined LD blocks from LDetect? It may be that some loci are dropped.

[Captain-Pam]

Hi @sookwah-yee @quattro. it is strange, seeing the example, it used the gtex_v7.db. However, I downed GTEx v8.db from PredictDB website (mashr model) to created the focus.db file by using ‘FOCUS import‘ command. So I agree with @quattro , maybe the locus is not in the LD block from LDetect.

[sookwah-yee]

Hi @Captain-Pam and @quattro, thank you for sharing the information for what you did.
I would like to try using GTEx v8.db soon and I wonder which one did you use @Captain-Pam ? There are four different one under Mashr model. Also if I use the v8.db and do the focus.import, do I need to convert the RSID to the different format?
mashr_eqtl.tar: PrediXcan’s and S-PrediXcan’s support on expression
mashr_sqtl.tar: PrediXcan’s and S-PrediXcan’s support on splicing
gtex_v8_expression_mashr_snp_smultixcan_covariance.txt.gz: S-MultiXcan expression’s LD reference
gtex_v8_splicing_mashr_snp_smultixcan_covariance.txt.gz: S-MultiXcan splicing’s LD reference