similar to: How to check cy5 and cy3 values were lowess normalized

Could anyone please explain to me why the following writes nothing into "all.Rout" file? If the "for" loop is removed, t.test output can be written into "all.out". Thanks in advance. Minghua Yao ...... zz <- file("all.Rout", open="wt") sink(zz) for(i in 1:n) { Cy3<-X[,2*i-1]; Cy5<-X[,2*i]; t.test(Cy3, Cy5)

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 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

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

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 <-

Dear all, I need some help on matrix design and B statistics by using limma package. I want to compare gene expression in 2 groups of cDNA samples. The experiment compares 4 treated mice(#1,#2,#3,#4) and 4 control mice (#5,#6,#7,#8). The target file is FileName Cy3 Cy5 mice1.spot Control_#5 Treat_#1 mice2.spot Treat_#1 Control_#5 mice3.spot Control_#6 Treat_#2

Dear list members, I am analysing my microarray data using limma package. Now I encounter several problems. Looking forward to your suggestions! Question 1: During the process of background correction using method="normexp", four warning messages appeared as "NaNs produced in: log(x)" (as you can see in the program posted below). What does that mean? How will it effect the

Hi, I'm working with custom slides(Cy5) and working in the normalization of the arrays. I have three arrays (technical replicates). I have sucesfully normalized the data using vsn, however i would like to normalize using spike in controls. My controls are annotated as CTL-1 to x and i would like to do etiher a normalization by block per array or the mean of all the controls per array. The gal

The lowess() help page refers to documentation in "src/appl/lowess.doc". This was moved to "src/library/stats/src/lowess.doc" in 2007. This patch fixes it: Index: src/library/stats/man/lowess.Rd =================================================================== --- src/library/stats/man/lowess.Rd (revision 79137) +++ src/library/stats/man/lowess.Rd (working copy) @@

Hi, A lowess method is defined in our package for one of our S4 classes. To explicitely define the generic this is being used if (!isGeneric("lowess")) setGeneric("lowess", useAsDefault = lowess) This works fine for many other methods inherited from various R packages. In this case a warning is issued in R CMD check: * checking R code for possible problems ... NOTE

Just noticed nobody has commented on this, so I took a look, and I can't see the problem (2.1.0 looks the same as 2.1.1 to me). What is supposed to be wrong? Duncan Murdoch On 5/23/2005 2:35 PM, pelzc at ohsu.edu wrote: > Full_Name: Carl Pelz > Version: 2.1.0 & 2.0.1 > OS: Windows 2000 > Submission from: (NULL) (137.53.64.158) > > > # Paste this all into an R

hi: apologies for taking up everyone's time. my problem is probably documented somewhere, but I again cannot find it. (which reminds me: I cannot find a search engine that allows me to search the archives of this very useful mailing list.) * it seems that lines(lowess()) fails to plot certain line segments. (and, what does it do at the x-min and x-max of a data set?) Rather than

Hi All, I've been providing a generic version of lowess() in my 'gregmisc' library, along with a 'lowess.formula' and 'lowess.default'. Can/should these be moved into base? -Greg LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else

Hi there, I'm plotting some glass RI values just by plotting plot(x) then I put on my lowess smoother lines(lowess(x)) now I want to put on some 95% Confidence Interval bands of the lowess smoother, but don't know how?? Thanks -- Gareth Campbell PhD Candidate The University of Auckland P +649 815 3670 M +6421 256 3511 E gareth.campbell@esr.cri.nz gcam032@gmail.com [[alternative

This is not a "help" request, just an experience with R that I found amusing. I have a machine learning module that I teach which was originally all symbolic, but has a slowly growing numeric/statistical component. Today I taught a two part lecture on instance based methods for learning, with the first half being simple KNN, then kernel methods for regression. The second half was using

I don't really see the point. lowess() is a two-dimensional smoother only so the main point would only be to allow lowess(y ~ x, dat) instead of lowess(dat$x, dat$y). Bill V. -----Original Message----- From: r-devel-bounces@stat.math.ethz.ch [mailto:r-devel-bounces@stat.math.ethz.ch] On Behalf Of Warnes, Gregory R Sent: Wednesday, 21 January 2004 4:48 PM To: 'R-devel' Subject:

code: x <- rnorm(32) y <- rnorm(32) plot(x,y) lines(lowess(x,y),col='red') Now I need to sample the lowess function into matrix where one series will be X and other will be values of lowess at particular X. -- View this message in context: http://r.789695.n4.nabble.com/how-to-sample-lowess-loess-into-matrix-tp3053458p3053458.html Sent from the R help mailing list archive at

I am trying to change the attributes of the lowess lines fit to an xyplot command, but have been unsuccessful in my search of the online help. Right now, both the points and lowess line come out in the same color (blue). I am unsure how I can change the properties of the lowess line separately. xyplot ( SnowLineElevation ~ Year | Model, data = data, ylim = c(0,1800), type =