search for: waverley

...t;) plot(perf,col="grey82",lty=3) plot(perf,lwd=3,avg="vertical",spread.estimate="boxplot",add=TRUE) I can follow the code and plot without any problem. However, I don't know how to extract the averaged ROC area under curve value. Can someone help? Thanks. -- Waverley @ Palo Alto

Hi, In perl, to get a substring matching a particular pattern can be implemented like the following example: $x = "AAAA.txt"; if ($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 @ Palo Alto

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

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 Alto

...or of squence into 2 groups. For example: 1, 2, 3, 4 I want to have a group of 1, (2,3,4) (1,2), (3,4) (1,3), (2,4) (1,4), (2,3) (1,2,3), 4 (2,3), (1,4) ... Can someone help me as how to implement this? I get some imaginary problem when the sequence becomes large. Thanks much in advance. -- Waverley @ Palo Alto [[alternative HTML version deleted]]

...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? Thanks a lot in advance. -- Waverley @ Palo Alto

...I have a matrix a = matrix (1:16, 4, 4) b = c (2,3) I want to find out which rows of a, where a[,1] equals any values of b? I know that if b is only one value, e.g, b=2, then what I want is a[a[,1] == 2,] But what about if it is not one value but a vector of values? Thanks much in advance. -- Waverley @ Palo Alto

...idth using lwd parameter. However, when outline=TRUE, the thickness of the circle of the outliers is not proportionally changed when I change the line width of the whisker box. There must be another parameter for that. Unfortunately I don't know. please help and thanks much in advance. -- Waverley @ Palo Alto

...you can use ROCR package. Is there a package you can plot ROC curve for 2d classifiers? One of my colleagues asked me about this. I have been quite puzzled, conceptually, how you can do the ROC curve for 2d classifiers. Can someone share his/her knowledge or experience? Thanks in advance. -- Waverley @ Palo Alto

...together. I cannot by looking at the plot to find where 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

...w matrix , rather than explicitly assign like matrix (b, ncol=1). I have come across a couple of time, that when I try to check how many rows of the computed result matrix - nrow(,,,), because there is only one row, the program failed as R tried to interpret it as a list. Can some one help? -- Waverley @ Palo Alto [[alternative HTML version deleted]]

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 -- Waverley @ Palo Alto

...debug, e.g., I have a for loop at the beginning of the function code and want the code execution to jump through that for loop and set a break after that. How to do that? Is there a web site detailing the syntax of the debugging of R? Hopefully it would be similar to java or C syntax. Thanks. waverley [[alternative HTML version deleted]]

...m I have en counted. But the problem is that I have two data frame, one works and the other does not. Also if I don't run under perl and run directly R under shell, both works. Can someone help? I am running R-2.5.0 with RMySQL-0.5-11 and DBI0.2.3. I am using linux redhat ES4.0 64 bit. -- Waverley @ Palo Alto [[alternative HTML version deleted]]

...If I have only 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 wrote: > Hi, > > I have a question of the method as how to normalize the data sets > according to a set of the internal measurements. > > For example, I have performed two batches of experiments contrasting > two different conditions (positive versus negative conditions): one a...

...event it becomes a list? I am new and thanks much for the help. Browse[1]> (each.uaa.data[,2]) [[1]] [1] 152.3530 [[2]] [1] 264.7059 [[3]] [1] 583.3333 [[4]] [1] 323.3333 [[5]] [1] 292.549 [[6]] [1] 300 [[7]] [1] 104.1176 [[8]] [1] 246.6667 [[9]] [1] 242.5490 [[10]] [1] 212.9412 -- Waverley @ Palo Alto [[alternative HTML version deleted]]

...he online help most of the sample code assumes the database exists and transact with the table inside the database. Can someone 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

...ch that this set of features is analyzed simultaneously as "one group" for the power analysis and sample size estimation. I also knew samr package has some 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

...ld be R list or vector. For example, I want to select * from Atable where ID would equal to a members of R list or vector of "1, 2, 3". Here the ID list was generated inside R and then try to feed to mysql to call to get additional data sets. Can someone on the list help? Thanks. -- Waverley @ Palo Alto [[alternative HTML version deleted]]

...Any R guru or expression analysis guru who are familiar with pamr can help me? Given saying that, I hope pamr author can make a public function to plot this like the figure 5 in their PNAS paper. After they should encourage user to recreate their nice work through easy APIs. Thanks. -- Waverley @ Palo Alto -- Waverley @ Palo Alto