Re: [R] Please help me!!!! Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected
thanks ï¼now i reduce the number of the descriptors, It is ok. å¨2010-01-03ï¼Max Kuhn [via R] ml-node+997387-1292262...@n4.nabble.com åéï¼ -åå§é®ä»¶- å件人:Max Kuhn [via R] ml-node+997387-1292262...@n4.nabble.com åéæ¶é´:2010å¹´1æ3æ¥ æææ¥ æ¶ä»¶äºº:bbslover dlu...@yeah.net 主é¢:Re: [R] Please help me Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected Your data set has 217 predictors and 166 samples. If you read the vignette on feature selection for this package, you'll see that the default ranking mechanism that it uses for linear models requires a linear model fit. The note that: prediction from a rank-deficient fit may be misleading should tell you something. If it doesn't: the model fit is over determined and there is no unique solution, so many of the parameter estimates are NA. Either create a modified version of lmFuncs that suits your needs or remove variables prior to modeling (or try some other method that doesn't require more samples than predictors, such as the lasso or elasticnet). Max On Fri, Jan 1, 2010 at 10:14 PM, bbslover [hidden email] wrote: I am learning the package caret, after I do the rfe function, I get the error ,as follows: Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected In addition: Warning message: In predict.lm(object, x) : prediction from a rank-deficient fit may be misleading I try to that manual example, that is good, my data is wrong. I do not know what reanson? my code is : subsets-c(1:5,10,15,20,25) ctrl-rfeControl(functions=lmFuncs, method = cv, verbose=FALSE,returnResamp=final) lmProfile-rfe(trainDescr,trainY,sizes=subsets,rfeControl=ctrl) before it, I have do some pre-process and my data is in the attachment. Please help me. thank you! kevinhttp://n4.nabble.com/file/n996068/trainDescr.txt trainDescr.txt http://n4.nabble.com/file/n996068/trainY.txt trainY.txt -- View this message in context:http://n4.nabble.com/Please-help-me-Error-in-data-frame-x-retained-drop-FALSE-undefined-columns-selected-tp996068p996068.html Sent from the R help mailing list archive at Nabble.com. __ [hidden email]mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Max __ [hidden email]mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. View message @http://n4.nabble.com/Please-help-me-Error-in-data-frame-x-retained-drop-FALSE-undefined-columns-selected-tp996068p997387.html To unsubscribe from Please help me Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected,click here. -- View this message in context: http://n4.nabble.com/Please-help-me-Error-in-data-frame-x-retained-drop-FALSE-undefined-columns-selected-tp996068p997622.html Sent from the R help mailing list archive at Nabble.com. [[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] Please help me!!!! Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected
Your data set has 217 predictors and 166 samples. If you read the vignette on feature selection for this package, you'll see that the default ranking mechanism that it uses for linear models requires a linear model fit. The note that: prediction from a rank-deficient fit may be misleading should tell you something. If it doesn't: the model fit is over determined and there is no unique solution, so many of the parameter estimates are NA. Either create a modified version of lmFuncs that suits your needs or remove variables prior to modeling (or try some other method that doesn't require more samples than predictors, such as the lasso or elasticnet). Max On Fri, Jan 1, 2010 at 10:14 PM, bbslover dlu...@yeah.net wrote: I am learning the package caret, after I do the rfe function, I get the error ,as follows: Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected In addition: Warning message: In predict.lm(object, x) : prediction from a rank-deficient fit may be misleading I try to that manual example, that is good, my data is wrong. I do not know what reanson? my code is : subsets-c(1:5,10,15,20,25) ctrl-rfeControl(functions=lmFuncs, method = cv, verbose=FALSE,returnResamp=final) lmProfile-rfe(trainDescr,trainY,sizes=subsets,rfeControl=ctrl) before it, I have do some pre-process and my data is in the attachment. Please help me. thank you! kevin http://n4.nabble.com/file/n996068/trainDescr.txt trainDescr.txt http://n4.nabble.com/file/n996068/trainY.txt trainY.txt -- View this message in context: http://n4.nabble.com/Please-help-me-Error-in-data-frame-x-retained-drop-FALSE-undefined-columns-selected-tp996068p996068.html Sent from the R help mailing list archive at Nabble.com. __ 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. -- Max __ 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] Please help me!!!! Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected
thanks, I have reduce the number of descriptors, and the erroe is none, my major is qsar, but what is the criterion to select descritors, and how many descriptors should be selected, It is a problem, I calculate my descriptors troungh E-dragon, and apply the wonderful package caret,but my result is poor, how can i improve my performance? Max is an expert in this field I think ,can you give me some suggestion in how can I well learn QSAR and build the perfect models based on nonlinear and linear. Here, only myself do QSAR research study lonely, and I have no some software to calculate descriptors except free ons, I just know e-dragon, have others? and good tools to do QSAR? thank you again. kevin! Max Kuhn wrote: Your data set has 217 predictors and 166 samples. If you read the vignette on feature selection for this package, you'll see that the default ranking mechanism that it uses for linear models requires a linear model fit. The note that: prediction from a rank-deficient fit may be misleading should tell you something. If it doesn't: the model fit is over determined and there is no unique solution, so many of the parameter estimates are NA. Either create a modified version of lmFuncs that suits your needs or remove variables prior to modeling (or try some other method that doesn't require more samples than predictors, such as the lasso or elasticnet). Max On Fri, Jan 1, 2010 at 10:14 PM, bbslover dlu...@yeah.net wrote: I am learning the package caret, after I do the rfe function, I get the error ,as follows: Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected In addition: Warning message: In predict.lm(object, x) : prediction from a rank-deficient fit may be misleading I try to that manual example, that is good, my data is wrong. I do not know what reanson? my code is : subsets-c(1:5,10,15,20,25) ctrl-rfeControl(functions=lmFuncs, method = cv, verbose=FALSE,returnResamp=final) lmProfile-rfe(trainDescr,trainY,sizes=subsets,rfeControl=ctrl) before it, I have do some pre-process and my data is in the attachment. Please help me. thank you! kevin http://n4.nabble.com/file/n996068/trainDescr.txt trainDescr.txt http://n4.nabble.com/file/n996068/trainY.txt trainY.txt -- View this message in context: http://n4.nabble.com/Please-help-me-Error-in-data-frame-x-retained-drop-FALSE-undefined-columns-selected-tp996068p996068.html Sent from the R help mailing list archive at Nabble.com. __ 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. -- Max __ 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. -- View this message in context: http://n4.nabble.com/Please-help-me-Error-in-data-frame-x-retained-drop-FALSE-undefined-columns-selected-tp996068p997526.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] Please help me!!!! Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected
I am learning the package caret, after I do the rfe function, I get the error ,as follows: Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected In addition: Warning message: In predict.lm(object, x) : prediction from a rank-deficient fit may be misleading I try to that manual example, that is good, my data is wrong. I do not know what reanson? my code is : subsets-c(1:5,10,15,20,25) ctrl-rfeControl(functions=lmFuncs, method = cv, verbose=FALSE,returnResamp=final) lmProfile-rfe(trainDescr,trainY,sizes=subsets,rfeControl=ctrl) before it, I have do some pre-process and my data is in the attachment. Please help me. thank you! kevin http://n4.nabble.com/file/n996068/trainDescr.txt trainDescr.txt http://n4.nabble.com/file/n996068/trainY.txt trainY.txt -- View this message in context: http://n4.nabble.com/Please-help-me-Error-in-data-frame-x-retained-drop-FALSE-undefined-columns-selected-tp996068p996068.html Sent from the R help mailing list archive at Nabble.com. __ 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.
