similar to: Question in Using sink function

All, Anybody can tell how to export a R plot onto Word (or Power Point)? Many thanks in advance. -MY

Hi, I have some microarray data, cy5 and cy3 values are in log2. Is there a way to check they have undergone lowess normalization ? Thanks Stanley [[alternative HTML version deleted]]

I would like to load ApoAI.RData. During the operation of reading this data an error occurs. There is also a problem with STF file. > library (limma) > load("ApoAI.RData") Warning message: 'RG' looks like a pre-2.4.0 S4 object: please recreate it > objects() [1] "RG" > names(RG) [1] "R" "G" "Rb"

Hello, I am not only interested in finding out which genes are the most highly up- or down-regulated (which I have done using the linear models and Bayesian statistics in Limma), but I also want to know which genes are consistently highly transcribed (ie. they have a high intensity in the channel of interest eg. Cy5 or Cy3 across the set of experiments). I might have missed a straight forward

Hello, I have R1.9.0 under Windows XP. My program plots several plots using x11() par(cex = 0.75) ...... x11() par(cex = 0.75) ...... x11() par(cex = 0.75) ...... x11() par(cex = 0.75) ...... Sometimes, one of them generates a small frame only with title area "R graphics: Device X (ACTIVE)". The message in the console window is Error in plot.new() : Figure margins too large

Hi, all, I want to use lowess(x, y) where x and y are vectors of length of 4000+. In fact, x and y are log of some vectors. So, some of the elements are NaN. lowess() can not take away those elements then do the fitting. It will give the error message and do nothing. 1. Can anybody tell me how to get rid of those NaN's and use lowess()? 2. How to get the LOWESS fitting values for any

Dear all, I have the following output generated by linear regression. Since there is only one regression intercept and one slope for one set of data, what is the meaning of std. error for intercept and that of slope? Thanks in advance. Sincerely, Minghua > data(thuesen) > attach(thuesen) > lm(short.velocity~blood.glucose) Call: lm(formula = short.velocity ~ blood.glucose)

Hi, Is there any function that can arrange a character in alphabetic order? Thanks for answer -MY [[alternative HTML version deleted]]

Hello sir: As to the "variance stabilization" method which is applied in the "vsn"package under R environment,here's a question about the ratio of the 2 channels: After applying vsn,we can get new_cy5 and new_cy3 intensity according to the original cy5 and cy3 intensity respectively. And the new_cy5 new_cy3 are similar with ln(intensity). But how can I calculate the

Gurus, I used predict(loess(Y~X)); where Y and X are of the same length. But there are same NA's in both Y and X. Those NA's are in the same locations in Y and X. The following is the error messageI got: Error in "[<-"(*tmp*, , i, value = predict(loess(Y~X))) : number of items to replace is not a multiple of replacement length If I replaced the NA's with a

Hi, Can anybody tell me how to open new a new window for plot()? Thanks. Minghua

Hi, Anyone can tell me how to generate "A01", "A02", ..., "A99"? paste("A", 1:99, sep="") generates "A1", "A2",..., "A99". This is not what I want. Thanks for the help. -MY [[alternative HTML version deleted]]

Hi, A simple question. I want to assign values to columns (or rows) of a matrix. It seems that AA[,i]<-A; # A is a vector or array; doesn't work. How can I accomplish that? Thanks alot. -MY

Hello, everyone, I don't quite understand the following message: > TTT <- t.test(1:10, y=c(7:20)) > class(TTT) [1] "htest" > TTT@p.value Error: Trying to get slot "p.value" from an object whose class ("htest") is not defined > TTT$p.value [1] 1.855282e-05 Why the message says the class of TTT is not defined while class(TTT) gets

Dear all, I have a question about limmaGUI that is usually run in R environment. My problem is loading data into the programm. I have 6 gpr files that apparently are not compatible with limma. Everytime I'm trying to load the data (including a RNA targets file, an error appears:Error reading files. that I'm not sure,but seems to have something to do with the format of my files

Dear all, Could anyone please tell me how to sort a matrix or a data frame against a column/row/component? Many thanks. -MY

All, I am new in R. I found sqlSave() doesn't work for our Oracle9i. The following was the message: > sqlSave(channel, USArrests, rownames="state") Error in sqlColumns(channel, tablename) : USArrests : table not found on channel Check case parameter in odbcConnect > sqlQuery() works OK. Please help. Thanks. -MY

Dear all, I am a newbie in R. I encounter a problem as follows. I have 2 vectors X and Y that have a equal length of several thousand. I see Y as the function of X. Both of them are random. X is not arrranged in any order. Of course, I do plot(X,Y). Now, I want to use a sliding narrow window to run over each X, then calculate the variances within that window. Anyone knows easy way in R to do

Hi, I have a rather complex xml document that I am attempting to parse based on attributes: <Manifest xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <!-- eName : name of the element. eValue : value of the element. --> <OutputFilePath>D:\CN_data\Agilent\Results\</OutputFilePath> <FilesList> <File>

Dear R-Help, I am using the LIMMA User's Guide 5 January 2007 PDF version. For the example show in Section 7.4 DIRECT TWO-COLOR DESIGNS (pgs. 33-34), I could not grasp the rationale in developing the contrast.matrix with these R statements (">" indicates the R command prompt): > contrast.matrix <-