Re: [R] R IMA sitetest problem
Got exactly the same issue as you.
did you sort it out?
in addition to your error I had this error at the IMA.methy450PP stage I got
this:
Warning message:
In if (snpfilter != FALSE) { :
the condition has length > 1 and only the first element will be used
--
View this message in context:
http://r.789695.n4.nabble.com/R-IMA-sitetest-problem-tp4643126p4648252.html
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[R] nipals in the chemometrics package in R
Hello i need some precision about nipals in the chemometrics package in R . When i use nipals in chemometrics i obtain T and P matrix. I really don't understand what to do with these two matrix to obtain the scores for every the component (like in spss fo example) Comp1Comp2 Comp3 quest1 0,8434 0,54333 0,3466 quest2 0,665 0,7655 0,433 Thank you very much for your help (I know that X=TP+E)... But don't understand else __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nipals in the chemometrics package in R
Hello The solution maybe there but i need to compute it into R if someone can help me : (Previously store score vector t in score matrix T; store loading vector p in loading matrix P) that's done by nipals in chemometrics After use of nipals function you have T and P matrix First : "Calculate the residual matrix of X. Stop if the elements of Xres are very small because no further PCA components are reasonable" : Xres= X-u.b(T) u : improved score vector b: loading vector X : a mean-centered matrix Second : Replace X with Xres and continue with step 2 (with nipals chemometrics...) for calculation of the next PCA component. If someone can help me ? Thank's a lot 2011/12/1 zz dd > Hello > i need some precision about nipals in the chemometrics package in R . > > When i use nipals in chemometrics i obtain T and P matrix. > > I really don't understand what to do with these two matrix to obtain > the scores for every the component (like in spss fo example) > > Comp1Comp2 Comp3 > quest1 0,8434 0,54333 0,3466 > quest2 0,665 0,7655 0,433 > > Thank you very much for your help > (I know that X=TP+E)... But don't understand else > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nipals in the chemometrics package in R
Thank you for your brevity you don't have to say more things to show who you are. Else if you don't understand what we are talking about, you shouldn't be rude and insulting. May be you are quite young please take time to read Nonaka and Takeuchi and moreover Takanashi to uderstand the way to go from information to knowledge to wisdom that's quite useful for IS / IT and should bring you a bit of etiquette. *I have a dream* *that one day this nation will rise up and live out the true meaning of its creed : We hold these truths to be self-evident : that all men are created equal.* Have a nice day. 2011/12/5 Jeff Newmiller > This is not a homework help list. > --- > Jeff NewmillerThe . . Go Live... > DCN:Basics: ##.#. ##.#. Live > Go... > Live: OO#.. Dead: OO#.. Playing > Research Engineer (Solar/BatteriesO.O#. #.O#. with > /Software/Embedded Controllers) .OO#. .OO#. rocks...1k > --- > Sent from my phone. Please excuse my brevity. > > zz dd wrote: > > >Hello > >The solution maybe there but i need to compute it into R if someone can > >help me : > >(Previously store score vector t in score matrix T; store loading > >vector p > >in loading matrix P) that's done by nipals in chemometrics > >After use of nipals function you have T and P matrix > > > >First : "Calculate the residual matrix of X. Stop if the elements of > >Xres > >are very small > >because no further PCA components are reasonable" : > >Xres= X-u.b(T) > > > >u : improved score vector > >b: loading vector > >X : a mean-centered matrix > > > >Second : Replace X with Xres and continue with step 2 (with nipals > >chemometrics...) for calculation of the next PCA > >component. > > > >If someone can help me ? > >Thank's a lot > > > > > >2011/12/1 zz dd > > > >> Hello > >> i need some precision about nipals in the chemometrics package in R . > >> > >> When i use nipals in chemometrics i obtain T and P matrix. > >> > >> I really don't understand what to do with these two matrix to obtain > >> the scores for every the component (like in spss fo example) > >> > >> Comp1Comp2 Comp3 > >> quest1 0,8434 0,54333 0,3466 > >> quest2 0,665 0,7655 0,433 > >> > >> Thank you very much for your help > >> (I know that X=TP+E)... But don't understand else > >> > > > > [[alternative HTML version deleted]] > > > >__ > >R-help@r-project.org mailing list > >https://stat.ethz.ch/mailman/listinfo/r-help > >PLEASE do read the posting guide > >http://www.R-project.org/posting-guide.html > >and provide commented, minimal, self-contained, reproducible code. > > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nipals in the chemometrics package in R
Thank's Pedro Madrones, you're right that i have removed my name of the email (because of Spam, and datas that i can't remove on the net). Ok, i explain a bit more : X is a centred matrix. PCA summarise all variation of X into a few new variables called scores T.These new variables are linearly weighted combinations of the original X-variables. The loadings P contain the weights used for each X variable and thus reveal the influence of individual X-variables. Is it ok ? That's what give the nipals function of chemometrics package. It's just that i don't understand how to use The T and P matrix to have the component matrix. i don't need explainations how to obtain P and T But in how to do E = X tp. But maybe it's not there for this kind of questions, i am not from chemometrics science. *** Johannes E. S. 2011/12/5 Pedro Mardones > Perhaps you can try the examples given in > http://www.jstatsoft.org/v18/i02 for getting a better idea about how > the NIPALS algorithm works. BTW, yes,it looks like a homework question > specially when your user name is "zz dd " so you > can't be recognized. > > > > On Mon, Dec 5, 2011 at 9:27 AM, zz dd wrote: > > Thank you for your brevity you don't have to say more things to show who > > you are. > > Else if you don't understand what we are talking about, you shouldn't be > > rude and insulting. > > May be you are quite young please take time to read Nonaka and Takeuchi > and > > moreover Takanashi to uderstand the way to go from information to > knowledge > > to wisdom that's quite useful for IS / IT and should bring you a bit of > > etiquette. > > *I have a dream* *that one day this nation will rise up and live out the > > true meaning of its creed : We hold these truths to be self-evident : > that > > all men are created equal.* > > > > Have a nice day. > > > > 2011/12/5 Jeff Newmiller > > > >> This is not a homework help list. > >> > --- > >> Jeff NewmillerThe . . Go > Live... > >> DCN:Basics: ##.#. ##.#. Live > >> Go... > >> Live: OO#.. Dead: OO#.. Playing > >> Research Engineer (Solar/BatteriesO.O#. #.O#. with > >> /Software/Embedded Controllers) .OO#. .OO#. > rocks...1k > >> > --- > >> Sent from my phone. Please excuse my brevity. > >> > >> zz dd wrote: > >> > >> >Hello > >> >The solution maybe there but i need to compute it into R if someone can > >> >help me : > >> >(Previously store score vector t in score matrix T; store loading > >> >vector p > >> >in loading matrix P) that's done by nipals in chemometrics > >> >After use of nipals function you have T and P matrix > >> > > >> >First : "Calculate the residual matrix of X. Stop if the elements of > >> >Xres > >> >are very small > >> >because no further PCA components are reasonable" : > >> >Xres= X-u.b(T) > >> > > >> >u : improved score vector > >> >b: loading vector > >> >X : a mean-centered matrix > >> > > >> >Second : Replace X with Xres and continue with step 2 (with nipals > >> >chemometrics...) for calculation of the next PCA > >> >component. > >> > > >> >If someone can help me ? > >> >Thank's a lot > >> > > >> > > >> >2011/12/1 zz dd > >> > > >> >> Hello > >> >> i need some precision about nipals in the chemometrics package in R . > >> >> > >> >> When i use nipals in chemometrics i obtain T and P matrix. > >> >> > >> >> I really don't understand what to do with these two matrix to obtain > >> >> the scores for every the component (like in spss fo example) > >> >> > >> >> Comp1Comp2 Comp3 > >> >> quest1 0,8434 0,54333 0,3466 > >> >> quest2 0,665 0,7655 0,433 > >> >> > >> >> Thank you very much for your help > >> >> (I know that X=TP+E)... But don't understand else > >> >> > >> > > >> > [[alternative HTML version deleted]] > >&
Re: [R] nipals in the chemometrics package in R
That's solved. Just a cor between X and ti values. Thank you all. 2011/12/5 zz dd > Thank's Pedro Madrones, > you're right that i have removed my name of the email (because of Spam, > and datas that i can't remove on the net). > Ok, i explain a bit more : > > X is a centred matrix. > PCA summarise all variation of X into a few new variables called scores > T.These new variables are linearly weighted combinations > of the original X-variables. > The loadings P contain the weights used for each X variable and thus > reveal the influence of individual X-variables. > Is it ok ? > > That's what give the nipals function of chemometrics package. > > It's just that i don't understand how to use The T and P matrix to have > the component matrix. > > i don't need explainations how to obtain P and T But in how to do E = > X tp. > But maybe it's not there for this kind of questions, i am not from > chemometrics science. > > *** > Johannes E. S. > > > > > 2011/12/5 Pedro Mardones > >> Perhaps you can try the examples given in >> http://www.jstatsoft.org/v18/i02 for getting a better idea about how >> the NIPALS algorithm works. BTW, yes,it looks like a homework question >> specially when your user name is "zz dd " so you >> can't be recognized. >> >> >> >> On Mon, Dec 5, 2011 at 9:27 AM, zz dd wrote: >> > Thank you for your brevity you don't have to say more things to show who >> > you are. >> > Else if you don't understand what we are talking about, you shouldn't >> be >> > rude and insulting. >> > May be you are quite young please take time to read Nonaka and Takeuchi >> and >> > moreover Takanashi to uderstand the way to go from information to >> knowledge >> > to wisdom that's quite useful for IS / IT and should bring you a bit of >> > etiquette. >> > *I have a dream* *that one day this nation will rise up and live out the >> > true meaning of its creed : We hold these truths to be self-evident : >> that >> > all men are created equal.* >> > >> > Have a nice day. >> > >> > 2011/12/5 Jeff Newmiller >> > >> >> This is not a homework help list. >> >> >> --- >> >> Jeff NewmillerThe . . Go >> Live... >> >> DCN:Basics: ##.#. ##.#. Live >> >> Go... >> >> Live: OO#.. Dead: OO#.. Playing >> >> Research Engineer (Solar/BatteriesO.O#. #.O#. with >> >> /Software/Embedded Controllers) .OO#. .OO#. >> rocks...1k >> >> >> --- >> >> Sent from my phone. Please excuse my brevity. >> >> >> >> zz dd wrote: >> >> >> >> >Hello >> >> >The solution maybe there but i need to compute it into R if someone >> can >> >> >help me : >> >> >(Previously store score vector t in score matrix T; store loading >> >> >vector p >> >> >in loading matrix P) that's done by nipals in chemometrics >> >> >After use of nipals function you have T and P matrix >> >> > >> >> >First : "Calculate the residual matrix of X. Stop if the elements of >> >> >Xres >> >> >are very small >> >> >because no further PCA components are reasonable" : >> >> >Xres= X-u.b(T) >> >> > >> >> >u : improved score vector >> >> >b: loading vector >> >> >X : a mean-centered matrix >> >> > >> >> >Second : Replace X with Xres and continue with step 2 (with nipals >> >> >chemometrics...) for calculation of the next PCA >> >> >component. >> >> > >> >> >If someone can help me ? >> >> >Thank's a lot >> >> > >> >> > >> >> >2011/12/1 zz dd >> >> > >> >> >> Hello >> >> >> i need some precision about nipals in the chemometrics package in R >> . >> >> >> >> >> >> When i use nipals in chemometrics i obtain T and P matrix. >> >> >> >> >> >> I really don't und
