search for: marraynorm

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", cl...

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 script?...

...what capitalization style will be used for a given object, so capitalization is on the way to becoming a complication rather than a clarification. Here is a suggestion for a convention, which people can shoot down if they like: New-style classes: full capitalization, e.g., ExprSet, AffyBatch, MarrayNorm New-style generic functions: lower case first word, e.g., maNorm, normalize, rma, geneNames Old-style generic functions: leave as they are Non-generic functions: lowercase, with very sparing use of dot separaters Members of data classes: lowercase, possibly with dot separaters Function arguments:...

...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

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

...set of nodes. Joining of two graphs into a single graph. Functions to compute indegree and outdegree. --- limma: Substantial updates including support for more image analysis programs, new background correction methods, single channel normalization, support for import of exprSet and marrayNorm data objects, improved support for design and contrast matrices, new fitted model object class, within-gene multiple testing, Venn diagrams and generally a move to a simpler command style at the user level. --- matchprobes: A new package providing tools for working with probe seque...

...set of nodes. Joining of two graphs into a single graph. Functions to compute indegree and outdegree. --- limma: Substantial updates including support for more image analysis programs, new background correction methods, single channel normalization, support for import of exprSet and marrayNorm data objects, improved support for design and contrast matrices, new fitted model object class, within-gene multiple testing, Venn diagrams and generally a move to a simpler command style at the user level. --- matchprobes: A new package providing tools for working with probe seque...

Hello, I'm a french student working on a project concerning cDNA microarray. I've chosen to work with R and use the marrayClasses, marrayInput (...) packages. First, when I enter "library(marrayInput)", R warns me about a missing package called "utils" but I can't find it anywhere. Normally this package is installed when you install "base" package.

I'm tryng to use loess normalization function based on externals controls (like MSP) as in Yang et al.; 2002 paper. I work with bioconductor marrayNorm package. I identified my controls in the maControls structure of marrayLayout as a vector of 0 and 1. Is someone still use it ? for the moment I just have ... test <- maNormMain(manip.raw, f.loc = list(maNormLoess(x="maA", y="maM", z="maControls",subset=TRUE)))...

...ol_#6 Treat_#2 mice4.spot Treat_#3 Control_#7 mice5.spot Control_#8 Treat_#4 The first slide (mice1.spot) and the second slide(mice2.spot) are dye-swap. There is no common reference. There are 3 replicated spots of each gene on each array (384 genes in total). MA is an object of class marrayNorm, below is what I did. >design <- c(1,-1,1,-1,1) >cor <- duplicateCorrelation(MA,design,ndups=3) >cor$consensus.correlation [1] 0.506 >fit <- lmFit(MA,design,ndups=3,correlation=cor$consensus.correlation) >fit <- eBayes(fit) >topTable(fit,n=20,adjust="fdr&quot...

..., 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 GeneSpring data analysis program (GeneSpring) TOOLS: ======...