[R] help on naivebayes function in R
Hi, I have written a code in R for classifying microarray data using naive bayes, the code is given below: library(e1071) train-read.table(Z:/Documents/train.txt,header=T); test-read.table(Z:/Documents/test.txt,header=T); cl - c(c(rep(ALL,10), rep(AML,10))); cl - factor(cl) model - NaiveBayes(train,cl); pred-predict(model,test,type = raw); table(pred,cl); everything is working fine I am able to build the model and predict also but I am not able to get the confusion matrix using table function.its giving me the following error when I execute the line table(pred,cl) Error in sort.list(unique.default(x), na.last = TRUE) : 'x' must be atomic for 'sort.list' Have you called 'sort' on a list? I am not sure where I am going wrong. I want the confusion matrix using table function but I am not able to get it . Please help me . I will be really grateful .Thanks in advance. -Aadhithya -- View this message in context: http://r.789695.n4.nabble.com/help-on-naivebayes-function-in-R-tp2272720p2272720.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] how to tabulate the prediction value using table function for naive baiyes in R
Hi, I have written a code in R for classifying microarray data using naive bayes, the code is given below: library(e1071) train-read.table(Z:/Documents/train.txt,header=T); test-read.table(Z:/Documents/test.txt,header=T); cl - c(c(rep(ALL,10), rep(AML,10))); cl - factor(cl) model - naiveBayes(train,cl); pred-predict(model,test,type = raw); table(pred,cl); everything is working fine I am able to build the model and predict also but I am not able to get the confusion matrix using table function.its giving me the following error when I execute the line table(pred,cl) Error in table(pred,cl):all arguments must have the same length I am not sure where I am going wrong. I want the confusion matrix using table function but I am not able to get it . Please help me .Thanks in advance. -Aadhithya -- View this message in context: http://r.789695.n4.nabble.com/how-to-tabulate-the-prediction-value-using-table-function-for-naive-baiyes-in-R-tp2272742p2272742.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.
Re: [R] Need help for SVM code for microarray classification
Following is the error I am getting: Error in svm.default(train, cl) : Need numeric dependent variable for regression. My dataset looks like this in both training and testing: ALL ALL ALL ALL ALL ALL ALL ALL ALL ALL AML AML AML AML AML AML AML AML AML AML 0.9389671 1.0892019 0.24647887 0.57042253 0.10798122 0.58685446 0.0 0.5399061 0.20422535 0.2488263 0.84976524 0.7910798 0.39906102 0.5633803 1.0938967 0.86384976 1.0633802 0.7136150.5375587 0.07042254 1.7179487 0.0 0.32051283 0.012820513 0.0 0.0 0.2820513 0.98717946 0.26923078 0.07692308 0.0 0.0 0.24358974 0.0 0.0 0.46153846 0.0 0.20512821 0.20512821 0.0 1.4024506 0.20640905 0.10084826 0.09142318 0.037700284 0.07257304 0.1206409 0.14514609 2.0 0.11310085 0.030160226 0.15834118 0.00282752121.1630538 0.14137606 0.31479737 0.2544769 0.12629595 0.24222432 0.0028275212 first line Has the class whether it is ALL or AML class and from the next line I have the expression values is this the right way to give the dataset to R for SVM classification? Thanks a lot for immediate reply. I am really grateful. - Aadhithya -- View this message in context: http://r.789695.n4.nabble.com/Need-help-for-SVM-code-for-microarray-classification-tp2271652p2272045.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.
Re: [R] Need help for SVM code for microarray classification
Hello Steve Thanks for quick responses its really helping me out .Ya I made the necessary changes you had mentioned. I was not sure of that 'type' argument where u had told me to set it to SVM . Do you mean I have to give that argument in this line cl - c(c(rep(ALL,10), rep(AML,10))); and when I ran the code the following output I had got : result: pred ALL AML ALL 7 5 AML 3 5 Does this mean that 7 samples of ALL from test file has been classified as ALL and 5 samples of ALL are classified as AML and so on or is there any other way we can interpret this result . I am sorry I am troubling you a lot but seriously its a very timely help I am really thankful to you. -Aadhithya -- View this message in context: http://r.789695.n4.nabble.com/Need-help-for-SVM-code-for-microarray-classification-tp2271652p2272563.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.
Re: [R] Need help for SVM code for microarray classification
Hi Steve I had done one more thing I had taken the transpose of both my test and train files as given below: model- svm(t(train),cl); pred - predict(model,t(test)); And the result I had got is : Result: pred ALL AML ALL 10 0 AML 0 10 why is there a difference in the result which I had given in the before post?does this mean doing transpose classifies the samples better? or is there any reason for this? Thanks a ton in advance. -Aadhithya -- View this message in context: http://r.789695.n4.nabble.com/Need-help-for-SVM-code-for-microarray-classification-tp2271652p2272590.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.
Re: [R] Need help for SVM code for microarray classification
Hello Steve Thanks for quick responses its really helping me out .Ya I made the necessary changes you had mentioned. I was not sure of that 'type' argument where u had told me to set it to SVM . Do you mean I have to give that argument in this line cl - c(c(rep(ALL,10), rep(AML,10))); and when I ran the code the following output I had got : result: pred ALL AML ALL 7 5 AML 3 5 Does this mean that 7 samples of ALL from test file has been classified as ALL and 5 samples of ALL are classified as AML and so on or is there any other way we can interpret this result . I had done one more thing I had taken the transpose of both my test and train files as given below: model- svm(t(train),cl); pred - predict(model,t(test)); And the result I had got is : Result: pred ALL AML ALL 10 0 AML 0 10 why is there a difference in the result which I had given in the before post?does this mean doing transpose classifies the samples better? or is there any reason for this? I am sorry I am troubling you a lot but seriously its a very timely help I am really thankful to you. -Aadhithya -- View this message in context: http://r.789695.n4.nabble.com/Need-help-for-SVM-code-for-microarray-classification-tp2271652p2272658.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] Need help for SVM code for microarray classification
Hi I am Aadhithya I am trying to write a code to classify microarray data (AML and ALL) using SVM in R my code goes like this : library(e1071) train-read.table(Z:/Documents/train.txt,header=T); test-read.table(Z:/Documents/test.txt,header=T); cl - c(c(rep(ALL,10), rep(AML,10))); model- svm(train,cl); pred - predict(model,t(test)); table(pred,t(cl)); But I am not able to run it its giving me error . I will be really grateful if someone can help me.Thanks in advance -- View this message in context: http://r.789695.n4.nabble.com/Need-help-for-SVM-code-for-microarray-classification-tp2271652p2271652.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.
