search for: marray

In my package, I create a new method for plot with the following signature: setMethod("plot", signature(x="marrayNorm", y="formula"), plot.ma) where marrayNorm is a class defined in the marray package. After building and installing my package, I get the following warnings when I load my package (with library(maVis)): Warning messages: 1: In the method signature for function "plot"...

Dear R users, I'am using marray and Limma packages to analyze genepix output. 1) how can I filter bad spots from my data (data contains 3 types of bad spots). my experiment contains 12 samples and the bad spot are not associated to the same probes 2) how can I remove control probes from my data ? I'm sorry, i'm new with...

Hi, everyone, I ran the test case in "Introduction to the Bioconductor marrayInput package first. When I ran the session in (read.marrayRaw) I got the following error messages. Other sessions work well. The functions and errors are labled with blue and red respectively. >mraw <- read.Spot(path = datadir, layout = galinfo$layout, gnames = galinfo$gnames, target = swir...

Dear all, Trying to produce 4 maImage plots (marray package) on the same device (2 on the top and 2 on the bottom) with the layout() function or the split.screen() function, we are facing the following problem: it seems that maImage() does nt care about any of these 2 functions, and plots only one image at a time. Maybe this is inherent to this maI...

...;affyQCReport" [5] "annaffy" "annotate" "Biobase" "biomaRt" [9] "Biostrings" "DynDoc" "gcrma" "genefilter" [13] "geneplotter" "GenomicRanges" "hgu95av2.db" "limma" [17] "marray" "multtest" "vsn" "xtable" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11' Error in if (ok) { : missing value where TRUE/FALSE needed > biocLite...

...es" [9] "gal" "galfile" [11] "i" "readGalfile2" [13] "sample1" "ttest1" > grep("_gpr$",ls()) [1] 4 > ls()[4] [1] "fll92_1a_gpr" > class(ls()[4]) [1] "character" > class(fll92_1a_gpr) [1] "marrayRaw" attr(,"package") [1] "marray" I use the regular expression to get the name of the object I want, which is fll92_1a_gpr, the fourth element in ls() list. But i can't get the content of that object using ls()[4], which gives me a character object(having a double q...

...ifferent spans in the horizontal and vertical directions (the immediate reason being that replicate spots are laid out in the horizontal direction). Is it possible to do this in R? Functions like loess(stats) seem to apply the same span for all predictors, which carries over to functions like ma2D(marray). As an elementary second question, are there circumstances where one expects to see a substantial difference in the fits between say loess(y ~ x1 + x2) and loess(y ~ x1 * x2) with an interaction term (and if so, what are they)? Many thanks, _Taku Taku A. Tokuyasu, PhD UCSF Helen Diller Family...

...through image(graphics) is filled, I mean starting filling the graphical matrix by row from the upper-left rather than by the lower-left cell... In many cases, it can be usefull to have a representation of the data spatialy corresponding to a real support, as it is the case with the function image(marray) from Bioconductor packages, which fills the graphical matrix by row from upper-left, but just handles marrayRaw or marrayNorm objects. Of course, I could reorder the matrix, but it's heavier than with an already available function if it exists... Thanks a lot for help BUHARD Olivier

Hello R-Users! I'm using a heatmap to visualize a matrix of values between -1 and 3. How can I set the colors so that white is zero, below zero is blue of increasing intensity towards -1 and above zero is red of increasing intensity towards red? I tried like this (using the marray and gplots packages from bioconductor): mcol <- maPalette(low="blue", mid="white", high="red",k=100) heatmap.2(my_matrix, col=mcol) But white does not correspond to zero, because the value distribution is not symmetrical, so that zero is not in the middle. Is it s...

...uot; "affyPLM" "annaffy" "annotate" [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" [11] "geneplotter" "hgu95av2.db" "limma" "marray" "matchprobes" [16] "multtest" "ROC" "vsn" "xtable" "affyQCReport" Anything that I install after this gives me the same error. I tried uninstalling R 2.7.0 and installing R 2.6.2, and performing t...

I'm working on some heatmaps, and the person I'm working with would prefer a red-black-green color palette (red denoting gene induction and green denoting gene repression). Does such a palette exist already? If not, is there an easy way to create one? Thanks, Jake

...quot;spot" format. They do not automatically get unzipped when required. I have checked that read.maimages (in limma) does not, unless I have missed something, have an option for reading zipped files. Is there any way to get around this without substantially complicating the exposition in marray-notes.pdf (also in the inst/doc subdirectory)? John Maindonald email: john.maindonald at anu.edu.au phone : +61 2 (6125)3473 fax : +61 2(6125)5549 Centre for Mathematics & Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National...

...mes to file in: write.table(q, "C:/Temp/op.xls", 2: appending column names to file in: write.table(q, "C:/Temp/op.xls", 3: appending column names to file in: write.table(q, "C:/Temp/op.xls", I am using R2.2.1 windows version. I tried using write.xls from "marray" package but no success. Thanx in advance. Sachin __________________________________________________ [[alternative HTML version deleted]]

Dear all, I am finding difficulty in the following, I would like to create an empty matrix e.g. 10x10 of 0s and sequentially fill this matrix with randomly placed a 1s until it is saturated. Producing 100 matrices of sequentially increasing density., This process needs to be randomized 1000 times., I assume i should run this along the following lines, 1) Create 1000 matrices all zeros, 2) add

Hi Folks, Can anyone give me the tip I've been groping for with the following question:? mu: kx2x2x2 array of reals corresponding to means of k RVs at the combinations of values (1,2)x(1,2)x(1,2) of dichotomous variables F1,F2,F3 mu prints out as k rows (one for each Xi) of 8 numbers M: N x (3+k) matrix of cases. The first 3 cols are values of

...ot;tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: convert seanlib gplots gdata gtools geneplotter annotate Biobase marray limma firstlook "1.1.9" "1.0" "2.0.0" "2.0.0" "2.0.0" "1.4.3" "1.5.1" "1.4.22" "1.5.24" "1.8.1" "1.4" Matt McCall

Hi, I am drawing a heat map using gplots of R package. The file (new4) is having values 0 and 1 only. library(gplots) library(marray) x=read.table("new4", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c("black","red"))(256), #col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("row"), scale = c("row"), na.rm=TRUE, trace...

Dear Sir/Madam, I could succesfully normalise my microarray data using marrayNorm package. However, i have not been able to get normalised red and green channel intensities through R package. Is there a possibility to write a formula to calculate back the red and green channel intensities after normalisation of the data. Do I need to incorporate this formula in my R scr...

Hello everyone. There is a new competition, outlined on the blog dataists<http://www.dataists.com/2010/10/using-data-tools-to-find-data-tools-the-yo-dawg-of-data-hacking/>, inviting us to analyse statistics of the use of R packages (collected from 52 R users), to create a R-package suggestion engine for ourselves. Since I noticed several bloggers already wrote about it (as I have detailed

...in limma -- Annotation tools (Resourcer, GOstat, goTools, ontoTools) -- Improved interfaces (limmaGUI, affylmGUI, webbioc, -- MAGE file processing (RMAGEML) -- affymetrix processing: many improvements, gcrma, affypdnn (probe-dependent nearest neighbors), affyPLM (probe-level models). -- marray (next generation of the depreciated marrayClasses, marrayNorm, marrayPlots, marrayTools packages) -- General analysis tools (rama, qvalue, pickgene, EBarrays, impute, pamr, bim, ) -- QA/QC (arrayMagic, arrayQuality, LPE) -- sequence analysis (pairseqsim, Biostrings) -- interface to the Ge...