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 <teb...@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 <dwinsem...@comcast.net> > *Sent:* Thursday, September 8, 2022 8:51 PM > *To:* Bogdan Tanasa <tan...@gmail.com> > *Cc:* Ebert,Timothy Aaron <teb...@ufl.edu>; r-help <r-help@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 <tan...@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 <teb...@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-boun...@r-project.org> On Behalf Of Bogdan Tanasa > Sent: Sunday, August 28, 2022 8:55 PM > To: David Winsemius <dwinsem...@comcast.net> > Cc: r-help <r-help@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 <dwinsem...@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@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 > 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