Not to worry, the second article did not have equations either. It had a couple
bits of code and a github link to icechip (page 3295).
I got through the paywall using a link through the University of Florida library
system.
Maybe the linked papers include citations that describe the analysis in enough
detail, but that effort exceeds my time limit for this activity.
Tim
From: David Winsemius <dwinsemius at comcast.net>
Sent: Thursday, September 8, 2022 8:51 PM
To: Bogdan Tanasa <tanasa at gmail.com>
Cc: Ebert,Timothy Aaron <tebert at ufl.edu>; r-help <r-help at
r-project.org>
Subject: Re: [R] confidence intervals
[External Email]
The first article had no code and did not describe a formula that I could find
which matched your code. The second article is behind a paywall.
?
David.
Sent from my iPhone
On Sep 3, 2022, at 3:39 PM, Bogdan Tanasa <tanasa at
gmail.com<mailto:tanasa at gmail.com>> wrote:
?
Dear Aaron, David, and everyone,
Thank you again for your comments on my question related to the confidence
intervals. I am sorry for the late reply.
The definition of the 95 confidence intervals where our discussion originates
from has been proposed by the authors of these two articles (I am including the
links to the articles just to show that the formula has been published in a
methods article a while ago; the articles are in the field of biology though,
where not too many of you are part of, I guess). These authors have written the
scripts and they have made those available on github. I have asked a while ago
the authors why they have chosen this formula, however, I have not received any
reply. In any case, at this moment I will use the mathematical formulas
described in the articles :
https://www.cell.com/molecular-cell/fulltext/S1097-2765(15)00304-4<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cell.com%2Fmolecular-cell%2Ffulltext%2FS1097-2765(15)00304-4&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996716811%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vkeF5mjxFkAJtsshVbzOEblOakQVe9TUVG9WUy79KRI%3D&reserved=0>
https://www.nature.com/articles/s41596-019-0218-7<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41596-019-0218-7&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996716811%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QisH5QlhY699g3ExBEh89nrtR3H3ZX9AarqtvUMKzpw%3D&reserved=0>
Wishing everyone a good weekend,
Bogdan
On Sun, Aug 28, 2022 at 6:53 PM Ebert,Timothy Aaron <tebert at
ufl.edu<mailto:tebert at ufl.edu>> wrote:
I have a general dislike of "analysis emergencies." I would like to
see a data emergency wherein someone must cram 3 years of data collection into
18 months so that they have time to work out the correct analysis. I am sure
others would suggest working out how analyze the data before starting the
experiment.
Our business office gives this advice to faculty members: An emergency on your
part is not an emergency on our part.
How about starting by answering the questions posted by the people you are
hoping will help. Focus on David's middle paragraph. However, if you can
re-code everything to work, then it would seem that you already know the answer
and it might be simpler/faster to write the correct code.
You might spend some time looking for a scientific paper that uses that equation
for the confidence interval and thereby get some context to explain why the
equation is correct.
Tim
-----Original Message-----
From: R-help <r-help-bounces at r-project.org<mailto:r-help-bounces at
r-project.org>> On Behalf Of Bogdan Tanasa
Sent: Sunday, August 28, 2022 8:55 PM
To: David Winsemius <dwinsemius at comcast.net<mailto:dwinsemius at
comcast.net>>
Cc: r-help <r-help at r-project.org<mailto:r-help at r-project.org>>
Subject: Re: [R] confidence intervals
[External Email]
Hi David,
Thank you for your comments, and feed-back message. I am very happy to learn
from the experience of the people on R mailing list, and without any doubt, I am
very thankful to you and to everyone for sharing their knowledge. I do apologize
for any confusion that I have created unwillingly with my previous email.
About my previous email related to the confidence intervals: indeed I have
posted the question with a detailed description on stackoverflow, and the link
is listed below.
I have to admit that I have been in rush willing to have the suggestions of
R-help members by Monday (if that would have been possible), as I have to make a
decision at the beginning of this week on whether I need to re-code the shell
script in R. I have a deadline on Wed. The script itself is less important per
se, I have included it just to point our the origin of my question.
I do certainly respect the principles of online R-help community, and I would
very much appreciate if I could have your advice on the following :
shall a "R code related emergency" arise, would it be acceptable to
post the question on stackoverflow with the corresponding data tables and
detailed code, and to refer the posting on R-help mailing list ?
If it is acceptable at least for a single email, and if you do not mind, I could
mention the link to stackoverflow, inviting our members to read it, shall they
be comfortable with this topic.
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstackoverflow.com%2Fquestions%2F73507697%2Fconfidence-intervals-of-a-biological-assay%3Fnoredirect%3D1%23comment129816241_73507697&data=05%7C01%7Ctebert%40ufl.edu%7C0ba5d535471b46c05ec508da89592c20%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637973313343894313%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8sF7j4OCgH12qx4d8NCiw1%2FDbPa6nrui27S9C3ZNuL0%3D&reserved=0<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstackoverflow.com%2Fquestions%2F73507697%2Fconfidence-intervals-of-a-biological-assay%3Fnoredirect%3D1%23comment129816241_73507697&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996716811%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4QuLHm0fSa9LPG2Vnf%2BnisdfMfnJQ1Y0zEXWgIyE16w%3D&reserved=0>
Thanks a lot, have a good week !
~ Bogdan
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstackoverflow.com%2Fquestions%2F73507697%2Fconfidence-intervals-of-a-biological-assay%3Fnoredirect%3D1%23comment129816241_73507697&data=05%7C01%7Ctebert%40ufl.edu%7C0ba5d535471b46c05ec508da89592c20%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637973313343894313%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8sF7j4OCgH12qx4d8NCiw1%2FDbPa6nrui27S9C3ZNuL0%3D&reserved=0<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstackoverflow.com%2Fquestions%2F73507697%2Fconfidence-intervals-of-a-biological-assay%3Fnoredirect%3D1%23comment129816241_73507697&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996716811%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4QuLHm0fSa9LPG2Vnf%2BnisdfMfnJQ1Y0zEXWgIyE16w%3D&reserved=0>
On Sat, Aug 27, 2022, 6:52 PM David Winsemius <dwinsemius at
comcast.net<mailto:dwinsemius at comcast.net>>
wrote:
> You cross-posted this to StackOverflow and did not say so. ... and
> you posted in HTML Bad dog squared. I cast one of the close votes on
> SO, but here I can only say ... READ the Posting Guide.
>
> You also give no citation other than someone's Github files with
> minimal comments in that material. You should indicate whether this
> code has any solid support. Why do you think this code is something to
depend upon?
>
> After all, you been posting questions on R-help for several months.
> Don't you think you should make a good faith effort to understand the
> principles underlying this resource?
>
>
> --
>
> David.
>
> On 8/26/22 17:55, Bogdan Tanasa wrote:
> > Dear all,
> >
> > Although I know that it is not a statistics mailing list, given my
> > work
> on
> > ICeChIP
> >
> >
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgith
>
ub.com<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fub.com%2F&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996873045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=em3fMdYfIwItLsX5ueMZXs%2F76Gs8hevXHWEbmZdGvdg%3D&reserved=0>%2Fshah-rohan%2Ficechip%2Fblob%2Fmaster%2FScripts%2FcomputeHMDan
>
dError&data=05%7C01%7Ctebert%40ufl.edu<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2F40ufl.edu%2F&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996873045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OrK1X0ZajWbvB0b9rrFbqcyINBGOzWdx1DF6qsXFL6o%3D&reserved=0>%7C0ba5d535471b46c05ec508da8
> 9592c20%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C63797331334389431
> 3%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6
> Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9HOH72K0Lj30w7tE%2BMN
> oXakPbO1sasaujUTsnHFwDZo%3D&reserved=0
> >
> > I would appreciate to have the answer to a question :
> >
> > given two variables a and b (a and b can have 1000 paired-values)
> > and a calibration number "cal",
> >
> > why the 95 confidence interval has been calculated as such for each
> > value
> > a(i) and b(i) :
> >
> > 100 / cal * sqrt (( a/ (b^2) + (a^2) / (b ^3)) * 1.96
> >
> > Thank you,
> >
> > Bogdan
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org<mailto:R-help at r-project.org> mailing
list -- To UNSUBSCRIBE and more, see
> > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fst
> >
at.ethz.ch<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fat.ethz.ch%2F&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996873045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GwN4PEwjH8pLOmNxg4h3vri9lwSfOjI35T7NY3o%2BlUQ%3D&reserved=0>%2Fmailman%2Flistinfo%2Fr-help&data=05%7C01%7Ctebert%4
> >
0ufl.edu<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2F0ufl.edu%2F&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996873045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=XFiqLbwUEZIYxD6PakZ2wUon5WbMNq5M%2FExYV3NQyuc%3D&reserved=0>%7C0ba5d535471b46c05ec508da89592c20%7C0d4da0f84a314d76ace60a
> > 62331e1b84%7C0%7C0%7C637973313344050547%7CUnknown%7CTWFpbGZsb3d8eyJW
> > IjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C300
> >
0%7C%7C%7C&sdata=KfmZ6PvxUVrbCMzVZcz6S2H2sqfWQmw2WIZHERwKDEk%3D&
> > amp;reserved=0
> > PLEASE do read the posting guide
>
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r%2F&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996873045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iGxY98c0YGqMi53P9cCNaf7m02afdGomEqbmrItjYtg%3D&reserved=0>
>
-project.org<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fproject.org%2F&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996873045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LO6k5YzUAN4H3yMRL9k5qkOBj%2BNXq2M%2BAnKVqMiNJ%2Bk%3D&reserved=0>%2Fposting-guide.html&data=05%7C01%7Ctebert%40ufl.edu<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2F40ufl.edu%2F&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996873045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OrK1X0ZajWbvB0b9rrFbqcyINBGOzWdx1DF6qsXFL6o%3D&reserved=0>%
> 7C0ba5d535471b46c05ec508da89592c20%7C0d4da0f84a314d76ace60a62331e1b84%
> 7C0%7C0%7C637973313344050547%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwM
> DAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&
> sdata=127HvzZh7q9Xa7LaESHIEXIy3CdmUyQ3cxAVeOA%2Bukg%3D&reserved=0
> > and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
______________________________________________
R-help at r-project.org<mailto:R-help at r-project.org> mailing list -- To
UNSUBSCRIBE and more, see
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help&data=05%7C01%7Ctebert%40ufl.edu%7C0ba5d535471b46c05ec508da89592c20%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637973313344050547%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=KfmZ6PvxUVrbCMzVZcz6S2H2sqfWQmw2WIZHERwKDEk%3D&reserved=0<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814996873045%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=dOZN0X9vdJd481cVZUFSCTpKxP33qwxsDJHgHxn6eU4%3D&reserved=0>
PLEASE do read the posting guide
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r-project.org%2Fposting-guide.html&data=05%7C01%7Ctebert%40ufl.edu%7C0ba5d535471b46c05ec508da89592c20%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637973313344050547%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=127HvzZh7q9Xa7LaESHIEXIy3CdmUyQ3cxAVeOA%2Bukg%3D&reserved=0<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r-project.org%2Fposting-guide.html&data=05%7C01%7Ctebert%40ufl.edu%7Cb8ea3424c9174ac48ecc08da91fd737e%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637982814997029285%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2FpbdlAPXXtKg%2BRllG45yD4fm9NoPhxjgPSBwF%2BFCpyM%3D&reserved=0>
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]