[R] machine learning on ordered (ranked) feature

Hi, there: just a little bit off-topic: any algorithm in classification is good for ordered features, like all variables used are 1, 2, 3,...; not really continuous but ordered. i tried random forest and dlda already. thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you

Re: [R] off-topic: better OS for statistical computing

, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] PCA IN R

hi, A very quick search of PCA in R results in a lot of packages involving that function. Just wondering which one is generally used for fat data like microarray, esp. when the number of features is really big? Thanks for comments -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you

[R] how to calculate mean into a list

Dear Listers: I have this task and suppose a0 is a list of 10 data.frames, I want to calculate like this (a0[[1]]+a0[[2]]+..+a[[10]])/10 Thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

Re: [R] finding the row(s) for a date in a data frame

]] __ R-help@stat.math.ethz.ch 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. -- Weiwei Shi, Ph.D Research

Re: [R] Is there any good tools to facilitate us to create R functions?

commented, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] Urgent Help needed

@stat.math.ethz.ch 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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did

Re: [R] Formula in lm inside lapply

http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help

[R] feature's contribution into classification

is the discrimant result $x? -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] write.table

] Behalf Of Weiwei Shi Sent: August 10, 2007 12:41 PM To: r-help@stat.math.ethz.ch Subject: [R] write.table Hi, I am always with this qustion when I tried to write a data.frame with row.names and col.names. I have to re-make the data frame to let its first column be the rownames and let

[R] write.table

that? thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] a question on lda{MASS}

On 8/9/07, Weiwei Shi [EMAIL PROTECTED] wrote: hi, assume val is the test data while m is lda model value by using CV=F x = predict(m, val) val2 = val[, 1:(ncol(val)-1)] # the last column is class label # col is sample, row is variable then I am wondering if x$x == (apply(val2*m$scaling

[R] a question on lda{MASS}

?) times val data and sum is the discrimant result $x? Thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] clustering on Trinary data

/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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

Re: [R] apply a function to loop through

, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] Installing packages...

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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed

Re: [R] dlda{supclust} 's output

-- Marcel Dettling Phone: +41 79 489 72 04 E-Mail: [EMAIL PROTECTED] Web:http://stat.ethz.ch/~dettling -- - Original Message - From: Weiwei Shi [EMAIL PROTECTED] To: R Help R-help@stat.math.ethz.ch Cc: [EMAIL PROTECTED] Sent: Tuesday, May

[R] reinforce library to re-load

and update the list of currently loaded packages and do not reload a package which is already loaded. (Furthermore, if the package has a name space and a name space of that name is already loaded, they work from the existing names space rather than reloading from the file system.) Thanks. -- Weiwei

Re: [R] running saved scripts

://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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix

[R] how to plot this?

) AND multiple 2-D plots. I am not familar with R's plotting utilities. Thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https

[R] a string to enviroment or function

Hi, I am wondering how to make a function Fun to make the following work: t0 - (paste(hgu133a, ENTREZID, sep=)) xx - as.list(Fun(t0)) # make it work like xx-as.list(hgu133aENTREZID) thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed

Re: [R] a string to enviroment or function

. On 6/25/07, jim holtman [EMAIL PROTECTED] wrote: I think that you might want: t0 - (paste(hgu133a, ENTREZID, sep=)) xx - as.list(get(t0)) # make it work like xx-as.list(hgu133aENTREZID) On 6/25/07, Weiwei Shi [EMAIL PROTECTED] wrote: Hi, I am wondering how to make a function Fun

Re: [R] how to ave this?

one of my approaches is: x0 = sapply(mylist, cbind) and manipulate from x0 (x0[1:nrow(x0)/2, ] correponds to fc and the lower part is tt. but it is not neat way. On 6/22/07, Weiwei Shi [EMAIL PROTECTED] wrote: Hi, I have a list that looks like this: [[1]] fc tt 50

[R] how to ave this?

how to average it so that I have one matrix t0 at the end, and t0[1,1] = (0.075..+0.0204..)/2 Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch

Re: [R] merge

the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R

[R] source a specific function

workspace: i.e., I only change my workspace by adding one function from a R source file). Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch

[R] simulate null hypothesis

if it is alll right. BTW, is there any general package or I just need sample() to do that? (just tried to make my question on-topic:) thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

Re: [R] pretty report

I think my initial intention is to write multiple worksheets for multiple data frames. write.csv or write.table cannot do that. On 6/12/07, Robert A LaBudde [EMAIL PROTECTED] wrote: At 09:13 PM 6/12/2007, Don wrote: At 5:01 PM -0400 6/12/07, Weiwei Shi wrote: Dear Listers: I have

[R] pretty report

does not. So I am wondering if there is a package in R for generating good reports. I found package xtable but it seems (if not, please correct me) that it can only generate one table for one file. Thanks for any suggestions, -W -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you

Re: [R] pretty report

Just realized append=T might help for xtable, but I think it still not very pretty :) On 6/12/07, Weiwei Shi [EMAIL PROTECTED] wrote: Dear Listers: I have a couple of data frames to report and each corresponds to different condtions, e.g. conditions=c(10, 15, 20, 25). In this examples, four

[R] history in R.app on Mac

, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

Re: [R] history in R.app on Mac

in R.app you will see them. Or up and down arrows. R.app implements some extra features, such as multiline command retrieval. Through preference settings you can control if you want to see just a single ls() or multiple, etc. Rob On Jun 11, 2007, at 9:18 AM, Weiwei Shi wrote: hi, I

Re: [R] data mining/text mining?

]] __ R-help@stat.math.ethz.ch 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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did

[R] save intermediate result

hi, is there a way to save a R object into workspace instead of into a file during a running of function? thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help

Re: [R] save intermediate result

codes as followed have bugs, my f1 function cannot return anything, which means I have to re-run the time-consuming line again. thanks, Weiwei On 5/4/07, Joerg van den Hoff [EMAIL PROTECTED] wrote: On Fri, May 04, 2007 at 03:45:10PM -0400, Weiwei Shi wrote: hi, is there a way to save a R

[R] dlda{supclust} 's output

Hi, I am using dlda algorithm from supclust package and I am wondering if the output can be a continuous probability instead of discrete class label (zero or one) since it puts some restriction on convariance matrix, compared with lda, while the latter can. thanks, -- Weiwei Shi, Ph.D Research

[R] intersect more than two sets

Hi, I searched the archives and did not find a good solution to that. assume I have 10 sets and I want to have the common character elements of them. how could i do that? -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

Re: [R] intersect more than two sets

assume t2 is a list of size 11 and each element is a vector of characters. the following codes can get what I wanted but I assume there might be a one-line code for that: t3 - t2[[1]] for ( i in 2:11){ t3 - intersect(t2[[i]], t3) } or there is no such apply? On 4/24/07, Weiwei Shi

Re: [R] intersect more than two sets

hard to turn that back into a number) Hadley -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] Size of an object in workspace

http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help

Re: [R] Random Forest

, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

[R] simply this loop?

])}) Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] Is this a bug?

-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] My First Function: cryptic error message

://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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed

Re: [R] how to reverse a list

Thanks all of you! But my next question is, how to improve R programming skills? I never have time in improving it but I feel I need to. Regards, W On 4/11/07, Seth Falcon [EMAIL PROTECTED] wrote: Weiwei Shi [EMAIL PROTECTED] writes: I forgot to add my bad solution here: reverseList

[R] problems in loading MASS

i386, darwin8.8.1 status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R version.string R version 2.4.1 (2006-12-18) Thanks -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did

Re: [R] problems in loading MASS

Science Hanover College On Apr 12, 2007, at 6:04 PM, Weiwei Shi wrote: Hi, there: After I upgraded my R to 2.4.1, it is my first time of trying to use MASS and found the following error message: install.packages(MASS) --- Please select a CRAN mirror for use in this session --- trying

[R] how to reverse a list

Hi, there: I am wondering if there is a quick way to reverse a list like this: t0 - list(a=1, b=1, c=2, d=1) reverst t0 to t1 t1 $`1` [1] a b d $`2` [1] c thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

Re: [R] how to reverse a list

:length(llid)) { each - llid[i] probes - d0[d0[,2]==each, 1] outlist - c(outlist, list(probes)) } names(outlist) - as.character(llid) outlist } On 4/11/07, Weiwei Shi [EMAIL PROTECTED] wrote: Hi, there: I am wondering if there is a quick way to reverse a list like this: t0 - list

Re: [R] how to reverse a list

thanks. split() is what I needed. On 4/11/07, jim holtman [EMAIL PROTECTED] wrote: try this: x - cbind(unlist(t0), names(t0)) x [,1] [,2] a 1 a b 1 b c 2 c d 1 d split(x[,2], x[,1]) $`1` a b d a b d $`2` c c On 4/11/07, Weiwei Shi [EMAIL PROTECTED] wrote

Re: [R] treenet

]] __ R-help@stat.math.ethz.ch 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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you

Re: [R] help with RandomForest classwt option

, they did not influence how the nodes are split. So I would go further in the above 2 options. Thank you again! Betty On 1/28/07, Weiwei Shi [EMAIL PROTECTED] wrote: Dear Betty: I could suggest 3 options: 1. try to use rf in fortran by following the linky below http

Re: [R] help with RandomForest classwt option

options. Thank you again! Betty On 1/28/07, Weiwei Shi [EMAIL PROTECTED] wrote: Dear Betty: I could suggest 3 options: 1. try to use rf in fortran by following the linky below http://www.stat.berkeley.edu/~breiman/RandomForests/cc_software.htm 2. make a wrapper function

Re: [R] help with RandomForest classwt option

]] __ R-help@stat.math.ethz.ch 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. -- Weiwei Shi, Ph.D Research

Re: [R] nnet question

and provide commented, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] enumerates all possible combinations

-guide.html and provide commented, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https

Re: [R] unique/subset problem

PROTECTED] wrote: Hi The pruned dataset has 8 unique genomes in it while the dataset before pruning has 65 unique genomes in it. However calling unique on the pruned dataset seems to return 65 no matter what. Any assistance in this matter would be appreciated. Thanks Lalitha --- Weiwei Shi

Re: [R] Why do return or visible don´t return my obj ekt?

, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] unique/subset problem

styp paer hinf vcho pmul buch ypes ecoliO157 xfas 60 Levels: aero aful aquae atum_D bbur bhal bmel bsub buch cace ccre cglu cjej cper cpneuA ... ypes --- Weiwei Shi [EMAIL PROTECTED] wrote: Then you need to provide more details about the calls you made

Re: [R] unique/subset problem

oh, i forgot, you can also convert factor into string like dataset$genome1 - as.character(dataset$genome1) so you don't have to use as.numeric(dataset$score) if you use as.is=T when you read.table HTH, weiwei On 1/26/07, Weiwei Shi [EMAIL PROTECTED] wrote: check ?read.table and add as.is=T

Re: [R] unique/subset problem

@stat.math.ethz.ch 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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know

[R] Cronbach's alpha

previous question about how to evaluate the consistency of a set of variables and about the total correlation (my 2 cent to answer the question). Is there any function in R to do that? Thank you very much! -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did

Re: [R] Cronbach's alpha

Message- From: r-help-bounces at stat.math.ethz.ch [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Weiwei Shi Sent: Wednesday, January 24, 2007 1:17 PM To: R R Subject: [R] Cronbach's alpha Dear Listers: I used cronbach{psy} to evaluate the internal

Re: [R] n step ahead forecasts

-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch

[R] which classification package in R can assign sample weight?

Hi, I am looking for some function implemented in R for classification, which has an option to allow me to assign sample weights in learning process? Implementation of a wrapper function is possible but I am curious if it already exists somewhere. Thanks, -- Weiwei Shi, Ph.D Research Scientist

Re: [R] which classification package in R can assign sample weight?

for any of these? On Tue, 23 Jan 2007, Weiwei Shi wrote: Hi, I am looking for some function implemented in R for classification, which has an option to allow me to assign sample weights in learning process? Implementation of a wrapper function is possible but I am curious if it already

Re: [R] Installing packages...

://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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed

[R] total correlation

dealing with discrete but also with continuous ones, it will be great ! thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https

Re: [R] logistic regression model + Cross-Validation

-guide.html and provide commented, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https

Re: [R] naive bayes help

, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] Help on variable ranking

deleted]] __ R-help@stat.math.ethz.ch 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. -- Weiwei

Re: [R] number of Nodes in Random Forest

://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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed

Re: [R] creating a list of lists

__ R-help@stat.math.ethz.ch 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. -- Weiwei Shi, Ph.D Research

Re: [R] memory limits in R loading a dataset and using the package tree

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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did

Re: [R] randomForest and missing data

. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] CV by rpart/mvpart

guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help

Re: [R] sapply problem

__ R-help@stat.math.ethz.ch 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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you

Re: [R] implementation of t.test

I think what i want is code in C or Java. But thanks though. On 12/11/06, Charles C. Berry [EMAIL PROTECTED] wrote: On Mon, 11 Dec 2006, Weiwei Shi wrote: Hi, there: for some reason, I need to look at t.test at coding level. Can anyone here suggest a place to start with? You mean how

[R] implementation of t.test

Hi, there: for some reason, I need to look at t.test at coding level. Can anyone here suggest a place to start with? thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

Re: [R] X-fold cross validation function for discriminant analysis

, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

[R] how to check a R object's property

. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

[R] history in Mac

) but found sooo many bugs with it... -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] predict.lda is missing ?

://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch

[R] colnames and get means for the columns with the same names

. thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] [BioC] colnames and get means for the columns with the same names

understand what you want to do. However, keep in mind that averaging the probesets representing the same gene may not represent the best solution. Also, if you search the archive a bit, I know this question has come up before. Sean -Original Message- From: Weiwei Shi [mailto

[R] margins in heatmap.2 and fond size for x-axis

-help and found there is no way to make it smaller since I am using the smallest = 1. Is there other way around? Thanks -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help

[R] gui for R

Hi, I met with many bugs when I used JGR and am looking for some other GUI's for Mac. I found SciViews-R by googling but it is only for windows to my best knowledge. Is there any other good gui like that, usable for Mac? Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you

[R] how to plot a data.frame?

hi, i have a data frame like this: 0.3 0.7 0.4 0.8 i am trying to plot this data frame and each cell is filled with different colors based on the value. Is there a function which can do this? thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did

[R] how to improve the efficiency of the following lapply codes

is needed, I will provide. thanks -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] how to improve the efficiency of the following lapply codes

: GenuineIntel cpu family : 15 model : 4 model name : Intel(R) Xeon(TM) CPU 3.60GHz stepping: 3 cpu MHz : 3591.419 cache size : 2048 KB thanks. On 10/25/06, Weiwei Shi [EMAIL PROTECTED] wrote: Hi, I have a series of lda analysis using the following lapply

[R] write a help file for my own function

Hi, I am wondering how I can write a help page for my own function so when I type ?myOwnfunc, then the help page will show up? thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

Re: [R] Progress Monitor in R

://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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix

[R] multiple consoles for R?

status major 2 minor 3.1 year 2006 month 06 day01 svn rev38247 language R version.string Version 2.3.1 (2006-06-01) thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed

[R] lda

hi, i am wondering if i could use lda$scaling (i.e. coeff) to evaluate variables' importance if all the x's are normalized before put into model? thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

[R] read.table

hi, how could I let the colname be the numbers instead of X plus numbers when I use read.table. Or there is an alternative way? thanks -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

Re: [R] read.table

thanks. i know how to go around it but i feel read.table should have something like that to disable the process of adding X to the header :) On 10/19/06, Marc Schwartz [EMAIL PROTECTED] wrote: On Thu, 2006-10-19 at 16:10 -0400, Weiwei Shi wrote: hi, how could I let the colname

[R] selection from a list

unlist and transform it into a data.frame to do selection, but I just want to learn if there is a way to do the list selection. thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III

Re: [R] cluster in R

St., London WC1E 6BT, phone +44 207 679 1698 [EMAIL PROTECTED], www.homepages.ucl.ac.uk/~ucakche -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch

[R] selectively load some objects from old workspace

. Is there an easier way to do like this: load some needed obj from old workspace, which has been implemented in R? thanks -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help

Re: [R] cluster in R

, Christian *** --- *** Christian Hennig University College London, Department of Statistical Science Gower St., London WC1E 6BT, phone +44 207 679 1698 [EMAIL PROTECTED], www.homepages.ucl.ac.uk/~ucakche -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I

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