[R] ROCR package question

#x27;t know how to extract the averaged ROC area under curve value. Can someone help? Thanks. -- Waverley @ Palo Alto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-p

[R] ROCR package question

se help me with the specifics of the above 3 questions. Use code instead of description would be helpful. Thanks a lot in advance. >Waverley, >use @ (instead of $) to extract the slots from the performance object (it's S4 >class system). >HTH, > Tobias On Sat, Jul 25, 2

[R] ROCR package question

? Thanks again for your kind help. Waverley, see help('performance-class') for a description of the slots. Your AUCs will be in p...@y.values, which itself is a list (one list element per run). Thus, you can use functions like unlist or s/lapply to access them, e.g. mea

[R] how to change the thickness of the lines of the boxplot outliers

parameter for that. Unfortunately I don't know. please help and thanks much in advance. -- Waverley @ Palo Alto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://

[R] how to change the thickness of the lines of the boxplot outliers

is kind of exaggerating but does show the case: the circles of outliers maintain the original length while the box becomes a black bulb. BTW: I am using linux redhat ES3.0 64 bit. R is 2.9.0 version. Thanks. >Hi >Waverley wrote: > Hi, > > I tried to use boxplot function. I am follo

[R] how to specify xlim in forestplot

specify xlim to define the x axis range. -- Waverley @ Palo Alto __ 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

[R] reference of object in R

Is there a way to pass an object by reference, like that seen in C, to a function in R? Thanks in advance! -- Waverley @ Palo Alto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

[R] pass object to function by reference in R

How? like that seen in C or C++. -- Waverley @ Palo Alto __ 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

[R] PAMR package question: How to plot Estimated probabilities for the training data and test data

APIs. Thanks. -- Waverley @ Palo Alto -- Waverley @ Palo Alto __ 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

[R] Question how to get up triangle of a matrix

Is there a simple way to get up triangle of a matrix and return as a vector? Thanks much. -- Waverley @ Palo Alto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

[R] question of R to do perl matching and matched string extraction

Hi, I want to extract some of the substring via pattern recognition. But I don't know how to do it in R. In perl: my $url = "/pages-cell.net/deepan/sony/"; if($url =~ m/\/(.*)\//g) { my @result = $1; return @result; } How does the same work in R? Thanks much in advance --

[R] Question about ROCR package

have Slots and one of the slot is "y.values". I type the object and I can see them in screen. But I want to extract the value for further programming and computation. I did a summary of the object and it is a "S4" mode which I don't understand. Can someone help? Thank

[R] how to perform power analysis and sample size estimation/projection using R

me utility you can do this but it seems does not work well in my situation. Please advise. Thanks a lot in advance for the help. -- Waverley @ Palo Alto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read t

[R] Question about normalization to a set of internal standards

be more accurate and robust to external noises. In general, I have a couple of matrices of the same dimensions and a reference matrix of values to be used as reference values to be normalize to. How should I do that? -- Waverley @ Palo Alto __ R-help

[R] How to normalize to a set of internal references

one house keeping gene, then I can divide every gene to that to normalize, then compare. But now I have 10 genes which can be utilized for normalization. I assume, the more reference genes to be used, the better, under this context. Can you help again? Thanks much in advance. Waverley w

[R] question about order

gt; order (z[1:4]) [1] 3 4 1 2 Can someone help? What is the problem here? Is this a R bug? How to order when handling a vector with repetitive values? -- Waverley @ Palo Alto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/lis

[R] how to create ROC curve for 2 dimensional classifiers

or experience? Thanks in advance. -- Waverley @ Palo Alto __ 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

[R] 1D classifier and 2D classifier

Hi, Is there any package which provides the functions of create one dimensional and/or Two dimensional classifiers? Thanks much. -- Waverley @ Palo Alto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

[R] question about matrix one column values matching a vector of values

. -- Waverley @ Palo Alto __ 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 get the value of aov summary into another variable

Hi, I have a question of aov. e.g. aov.ex = aov(x~y) summary(aov.ex) The aov summary will print to the screen. How can I extract the aov result, in particular the values of Pr(>F) and F value into a vector so that I can use them for other use? Thanks. -- Waverley @ Palo A

[R] question about anova

e discrepancies here? 3. a R program tech question: I need to extract the p value from the summary(aov.study) but not sure how to do it. looks like the summary is not a data frame or list. I need to take the p value and continue to use it in the R program for some other reports. Thanks much in adv

[R] need help explain the routine input parameters for seROC and cROC found in the R archive

(nn*na)) > se > } > > cROC<-function(AUC1,na1,nn1,AUC2,na2,nn2,r){ > se1<-seROC(AUC1,na1,nn1) > se2<-seROC(AUC2,na2,nn2) > > sed<-sqrt(se1^2+se2^2-2*r*se1*se2) > zad<-(AUC1-AUC2)/sed > p<-dnorm(zad) > a<-list(zad,p) > a > } >

[R] how to fetch rows with certain characteristics

to return a matrix of 1.2 1 2.0 2 1.3 3 Can someone suggest how to code for that? The second column can be of characters. Thanks much. -- Waverley @ Palo Alto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] how to fetch rows with certain characteristics

;])) > > Most of that is just formatting it in the way you requested. All you > need to compute the values is > > tapply(x[,1], x[,2], min) > > -Ista > > On Thu, Oct 29, 2009 at 1:47 AM, Waverley @ Palo Alto > wrote: >> Hi, >> >> I have a matrix, first

Re: [R] how to fetch rows with certain characteristics

(x) >> x.min <- tapply(x[,1], x[,2], min) >> x[x[,1] %in% x.min,] >> ## all matches >      V1 V2 > [1,] 1.2  1 > [2,] 1.2  1 > [3,] 2.0  2 > [4,] 1.4  3 >> ## unique matches >> unique(x[x[,1] %in% x.min,]) >      V1 V2 > [1,] 1.2  1 > [2,]

[R] question about function heatmap

the borders are. Can someone help? Essentially I want the dendro tree of the genes which are grouped after the clustering so that, e.g., I want to check whether genes clustered together are in the same pathway etc. Thanks in advance. -- Waverley @ Palo Alto

[R] Question to use R plot GO pie chart

Hi, I have a list of IPI gene IDs. I want to find out whether there is a package which can map the gene ontology to these IPIs, and plot the pie chart to demonstrate the molecular function distributions. The input is like the following gene IPI IDs: IPI:IPI8860.1|SWISS-PROT:Q9BXJ4-1|TREMBL:Q

[R] solicit help to read in 384 plate color image

each well. Is there a R package I can use for that? there is a package called "gitter" which is almost satisfying my needs. However, it can only read in grey values and no colors. If someone has the code, please share. -- Thanks. waverley [[alternative HTML versi

[R] program R using mac Xcode

Hi, I am starting to use Xcode a lot for C/C++ programming. Can you do R programming in Xcode? If can, how to configure to enable this? Much thank in advance. -- Waverley @ Palo Alto __ R-help@r-project.org mailing list https://stat.ethz.ch

[R] how to implement string pattern extraction in R

Hi, In perl, to get a substring matching a particular pattern can be implemented like the following example: $x = ".txt"; if ($x=~ /(.*?)\.txt/){ $prefix = $1; } So how to do the same thing in R? Can someone provide me the code sample? Thanks much in advance. -- Waverley @

Re: [R] how to implement string pattern extraction in R

code similar to that in perl to extract the prefix out of the string. Thanks much. On Sun, Aug 22, 2010 at 3:05 PM, Waverley @ Palo Alto wrote: > Hi, > > In perl, to get a substring matching a particular  pattern can be > implemented like the following example: > > $x = ".

[R] R program google search

Hi, Can someone help as how to use R to program google search in the R code? I know that other languages can allow or have the google search API If someone can give me some links or sample code I would greatly appreciate. Thanks. -- Waverley @ Palo Alto

Re: [R] R program google search

g the AJAX Search API. What about R? Thanks. On Fri, Sep 3, 2010 at 2:23 PM, Waverley @ Palo Alto wrote: > Hi, > > Can someone help as how to use R to program google search in the R > code?  I know that other languages can allow or have the google search > API > > If someone c

Re: [R] R program google search

ng} . "(" . $result->{url} . ")\n"; # etc } if(!$i){ print "Sorry, but there were no results.\n"; } On Fri, Sep 3, 2010 at 2:23 PM, Waverley @ Palo Alto wrote: > Hi, > > Can someone help as how to use R to program google search in the R > co

[R] User R to create MySQL database and table

provide me some sample code to create a database and table? Specifically create a database first, then create a table inside the database. Thanks a lot in advance. -- Waverley @ Palo Alto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman

[R] online recursive lssvm r package

Hi, I am looking for a R package which can do online recursive training, e.g. online recursive LSSVM algorithm. Can some one help? Thanks. Waverley. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https