[R] confidence intervals

Tue Sep 27 07:25:36 CEST 2022

HI everyone,

THe conversation below is already old :) Just wanted to add that I received
the explanations regarding the confidence intervals that are computed in
the article(s) that we have briefly discussed.
The answers have been posted on stackoverflow, com :
https://stats.stackexchange.com/questions/587641/confidence-intervals-of-a-biological-assay/587715#587715

Thanks again for your time and help,

Bogdan

On Fri, Sep 9, 2022 at 8:44 AM Ebert,Timothy Aaron <tebert using ufl.edu> wrote:

> 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 using comcast.net>
> *Sent:* Thursday, September 8, 2022 8:51 PM
> *To:* Bogdan Tanasa <tanasa using gmail.com>
> *Cc:* Ebert,Timothy Aaron <tebert using ufl.edu>; r-help <r-help using 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 using 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 using 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 using r-project.org> On Behalf Of Bogdan Tanasa
> Sent: Sunday, August 28, 2022 8:55 PM
> To: David Winsemius <dwinsemius using comcast.net>
> Cc: r-help <r-help using 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
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>
> On Sat, Aug 27, 2022, 6:52 PM David Winsemius <dwinsemius using 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>
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> > 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 using r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> >
>
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> and provide commented, minimal, self-contained, reproducible code.
>
>

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