"get_aggrscores" function produces "NAs"

[anitalakatos]

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

[federicomarini]

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]

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 GitHub<https://urldefense.com/v3/__https:/github.com/federicomarini/GeneTonic/issues/56*issuecomment-1784730633__;Iw!!CzAuKJ42GuquVTTmVmPViYEvSg!MsTtrbsUFRNwwKPVOQwqYCc-MnHPWNGq_DzsWGuDyUVjwKJtmE6MNAyQgg8a1hl9wlwh63ZWMPStQGCtqBXXM2pd$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AGMAUTHTPULMAVPNYYNGNELYB5SLZAVCNFSM6AAAAAA6UKT5POVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBUG4ZTANRTGM__;!!CzAuKJ42GuquVTTmVmPViYEvSg!MsTtrbsUFRNwwKPVOQwqYCc-MnHPWNGq_DzsWGuDyUVjwKJtmE6MNAyQgg8a1hl9wlwh63ZWMPStQGCtqCZAE1vq$>. 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: ***@***.*** .