search

federicomarini / GeneTonic

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
https://federicomarini.github.io/GeneTonic
Other
76 stars 8 forks source link

"get_aggrscores" function produces "NAs" #56

Open anitalakatos opened 1 year ago

anitalakatos commented 1 year ago

Dear Federico,

I want to apply "GeneTonic" to my dataset. When I used the "get_aggrscores," it returned "NAs" without generating error messages. I have attempted to debug the code but have been unable to identify the root cause of this issue. I would greatly appreciate your advice on resolving this issue.

Thank you in advance for your help and support.

Best regards, Anita

sessionINFO

res_enrich

federicomarini commented 1 year ago

Hi Anita, Please make sure that there are no NAs in the input data for the DESeq result object. I recall that having some there could lead to a specific geneset to be aggregated to NA.

In your case I see they are all NAs, tho - have a look that the conversion of the IDs via the annotation table is working correctly?

HTH, Federico

anitalakatos commented 1 year ago

Hi Federico,

Thank you for your help. It was the issue of ID conversion.

Thanks once again for your help. All the best, Anita

From: Federico Marini @.> Sent: Monday, October 30, 2023 1:46 AM To: federicomarini/GeneTonic @.> Cc: anitalakatos @.>; Author @.> Subject: Re: [federicomarini/GeneTonic] "get_aggrscores" function produces "NAs" (Issue #56)

Hi Anita, Please make sure that there are no NAs in the input data for the DESeq result object. I recall that having some there could lead to a specific geneset to be aggregated to NA.

In your case I see they are all NAs, tho - have a look that the conversion of the IDs via the annotation table is working correctly?

HTH, Federico

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/federicomarini/GeneTonic/issues/56*issuecomment-1784730633__;Iw!!CzAuKJ42GuquVTTmVmPViYEvSg!MsTtrbsUFRNwwKPVOQwqYCc-MnHPWNGq_DzsWGuDyUVjwKJtmE6MNAyQgg8a1hl9wlwh63ZWMPStQGCtqBXXM2pd$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AGMAUTHTPULMAVPNYYNGNELYB5SLZAVCNFSM6AAAAAA6UKT5POVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBUG4ZTANRTGM__;!!CzAuKJ42GuquVTTmVmPViYEvSg!MsTtrbsUFRNwwKPVOQwqYCc-MnHPWNGq_DzsWGuDyUVjwKJtmE6MNAyQgg8a1hl9wlwh63ZWMPStQGCtqCZAE1vq$. You are receiving this because you authored the thread.Message ID: @.***>

. WARNING - This email originated from outside of the UCI Health email system. Do not click any links and do not open attachments unless you can confirm the sender. PLEASE FORWARD SUSPICIOUS EMAILS TO: @.*** .