Mathelab
commented
5 years ago I'm assuming here that we can remove the adjvars column? Ewy
Closed steven-moore closed 5 years ago
Mathelab
commented
5 years ago I'm assuming here that we can remove the adjvars column? Ewy
steven-moore
commented
5 years ago We want to keep the adjvars column, so that investigators can see which metabolite they adjusted for.
For example, if I was testing for the relationship between metabolites and diabetes, I might want to adjust for glucose from the metabolomics data. This would allow me to see if the metabolites have predictive power above and beyond their correlation with glucose. Retaining the adjvars and showing “glucose” there allows me to track which models were and were not glucose adjusted.
S
From: Mathelab notifications@github.com Sent: Monday, December 10, 2018 3:43 PM To: CBIIT/R-cometsAnalytics R-cometsAnalytics@noreply.github.com Cc: Moore, Steve (NIH/NCI) [E] Steve.Moore@nih.gov; Assign assign@noreply.github.com Subject: Re: [CBIIT/R-cometsAnalytics] COMETS 1.4. When a metabolite is adjusted for, its array position is shown in adjvars instead of its name (#71)
I'm assuming here that we can remove the adjvars column? Ewy
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Mathelab
commented
5 years ago Yes of course, makes sense. Ewy
From: Steven Moore notifications@github.com Reply-To: CBIIT/R-cometsAnalytics reply@reply.github.com Date: Monday, December 10, 2018 at 4:19 PM To: CBIIT/R-cometsAnalytics R-cometsAnalytics@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, Comment comment@noreply.github.com Subject: Re: [CBIIT/R-cometsAnalytics] COMETS 1.4. When a metabolite is adjusted for, its array position is shown in adjvars instead of its name (#71)
We want to keep the adjvars column, so that investigators can see which metabolite they adjusted for.
For example, if I was testing for the relationship between metabolites and diabetes, I might want to adjust for glucose from the metabolomics data. This would allow me to see if the metabolites have predictive power above and beyond their correlation with glucose. Retaining the adjvars and showing “glucose” there allows me to track which models were and were not glucose adjusted.
S
From: Mathelab notifications@github.com Sent: Monday, December 10, 2018 3:43 PM To: CBIIT/R-cometsAnalytics R-cometsAnalytics@noreply.github.com Cc: Moore, Steve (NIH/NCI) [E] Steve.Moore@nih.gov; Assign assign@noreply.github.com Subject: Re: [CBIIT/R-cometsAnalytics] COMETS 1.4. When a metabolite is adjusted for, its array position is shown in adjvars instead of its name (#71)
I'm assuming here that we can remove the adjvars column? Ewy
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Mathelab
commented
5 years ago The adjvars and adjspec columns are the same, but one is the right value, so I’m removing adjvars. Adjspec is what the user has input so we’re OK.
Going to push shortly.
Best, Ewy
From: "Mathe, Ewy" Ewy.Mathe@osumc.edu Date: Monday, December 10, 2018 at 5:16 PM To: CBIIT/R-cometsAnalytics reply@reply.github.com, CBIIT/R-cometsAnalytics R-cometsAnalytics@noreply.github.com Cc: Comment comment@noreply.github.com Subject: Re: [CBIIT/R-cometsAnalytics] COMETS 1.4. When a metabolite is adjusted for, its array position is shown in adjvars instead of its name (#71)
Yes of course, makes sense. Ewy
From: Steven Moore notifications@github.com Reply-To: CBIIT/R-cometsAnalytics reply@reply.github.com Date: Monday, December 10, 2018 at 4:19 PM To: CBIIT/R-cometsAnalytics R-cometsAnalytics@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, Comment comment@noreply.github.com Subject: Re: [CBIIT/R-cometsAnalytics] COMETS 1.4. When a metabolite is adjusted for, its array position is shown in adjvars instead of its name (#71)
We want to keep the adjvars column, so that investigators can see which metabolite they adjusted for.
For example, if I was testing for the relationship between metabolites and diabetes, I might want to adjust for glucose from the metabolomics data. This would allow me to see if the metabolites have predictive power above and beyond their correlation with glucose. Retaining the adjvars and showing “glucose” there allows me to track which models were and were not glucose adjusted.
S
From: Mathelab notifications@github.com Sent: Monday, December 10, 2018 3:43 PM To: CBIIT/R-cometsAnalytics R-cometsAnalytics@noreply.github.com Cc: Moore, Steve (NIH/NCI) [E] Steve.Moore@nih.gov; Assign assign@noreply.github.com Subject: Re: [CBIIT/R-cometsAnalytics] COMETS 1.4. When a metabolite is adjusted for, its array position is shown in adjvars instead of its name (#71)
I'm assuming here that we can remove the adjvars column? Ewy
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Mathelab
commented
5 years ago Hi everyone,
I have pushed changes. Variables adjvars and adjspec are redundant. I have kept both in because I want to make sure one is not used downstream. Will clean this up later.
Best, Ewy
From: "Mathe, Ewy" Ewy.Mathe@osumc.edu Date: Monday, December 10, 2018 at 5:26 PM To: CBIIT/R-cometsAnalytics reply@reply.github.com, CBIIT/R-cometsAnalytics R-cometsAnalytics@noreply.github.com Cc: Comment comment@noreply.github.com Subject: Re: [CBIIT/R-cometsAnalytics] COMETS 1.4. When a metabolite is adjusted for, its array position is shown in adjvars instead of its name (#71)
The adjvars and adjspec columns are the same, but one is the right value, so I’m removing adjvars. Adjspec is what the user has input so we’re OK.
Going to push shortly.
Best, Ewy
From: "Mathe, Ewy" Ewy.Mathe@osumc.edu Date: Monday, December 10, 2018 at 5:16 PM To: CBIIT/R-cometsAnalytics reply@reply.github.com, CBIIT/R-cometsAnalytics R-cometsAnalytics@noreply.github.com Cc: Comment comment@noreply.github.com Subject: Re: [CBIIT/R-cometsAnalytics] COMETS 1.4. When a metabolite is adjusted for, its array position is shown in adjvars instead of its name (#71)
Yes of course, makes sense. Ewy
From: Steven Moore notifications@github.com Reply-To: CBIIT/R-cometsAnalytics reply@reply.github.com Date: Monday, December 10, 2018 at 4:19 PM To: CBIIT/R-cometsAnalytics R-cometsAnalytics@noreply.github.com Cc: "Mathe, Ewy" Ewy.Mathe@osumc.edu, Comment comment@noreply.github.com Subject: Re: [CBIIT/R-cometsAnalytics] COMETS 1.4. When a metabolite is adjusted for, its array position is shown in adjvars instead of its name (#71)
We want to keep the adjvars column, so that investigators can see which metabolite they adjusted for.
For example, if I was testing for the relationship between metabolites and diabetes, I might want to adjust for glucose from the metabolomics data. This would allow me to see if the metabolites have predictive power above and beyond their correlation with glucose. Retaining the adjvars and showing “glucose” there allows me to track which models were and were not glucose adjusted.
S
From: Mathelab notifications@github.com Sent: Monday, December 10, 2018 3:43 PM To: CBIIT/R-cometsAnalytics R-cometsAnalytics@noreply.github.com Cc: Moore, Steve (NIH/NCI) [E] Steve.Moore@nih.gov; Assign assign@noreply.github.com Subject: Re: [CBIIT/R-cometsAnalytics] COMETS 1.4. When a metabolite is adjusted for, its array position is shown in adjvars instead of its name (#71)
I'm assuming here that we can remove the adjvars column? Ewy
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steven-moore
commented
5 years ago Fixed and closed
If adjusting for a metabolite, the name is not shown onscreen. Similar to the issue #70 .