search for: vsn

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 ra...

I would like to announce that my DataLoad utility which can be found at: http://www.vsn-intl.com/genstat/downloads/datald.htm has been updated to support R data.frames. DataLoad reads a large variety of data formats (listed on the web page) and can convert these to ASCII or XDR data.frames. Only the Windows and Linux versions are up to date due to the fact that I no longer has access...

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 file is also loaded with all the array structure. Each block contains spike in con...

...verrides 1970-01-01 00:00:00.000000000 +0000 +++ xen-4.17.3+10-g091466ba55/debian/libxenmisc4.17t64.lintian-overrides 2024-02-05 22:37:18.000000000 +0000 @@ -0,0 +1 @@ +libxenmisc4.17t64: package-name-doesnt-match-sonames libxenmisc4.17 diff -Nru xen-4.17.3+10-g091466ba55/debian/libxenmiscV.install.vsn-in xen-4.17.3+10-g091466ba55/debian/libxenmiscV.install.vsn-in --- xen-4.17.3+10-g091466ba55/debian/libxenmiscV.install.vsn-in 2024-02-04 12:45:17.000000000 +0000 +++ xen-4.17.3+10-g091466ba55/debian/libxenmiscV.install.vsn-in 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -usr/lib/*/libxenctr...

...ot; "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() Using R version 2.11.1, biocinstal...

...ls like: targets file: Name FileName Target 0h1 GSM286031.CEL control 0h2 GSM286032.CEL control 0h3 GSM286033.CEL control 3h1 GSM286034.CEL three 3h2 GSM286035.CEL three 3h3 GSM286036.CEL three 6h1 GSM286037.CEL six 6h2 GSM286038.CEL six 6h3 GSM286039.CEL six library(affy) library(limma) library(vsn) pd <- read.AnnotatedDataFrame("er_for_affy.txt", header = TRUE, row.names = 2) pData(pd) #### load a <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose = TRUE) #### normalize x <- expresso(a, bg.correct = FALSE, normalize.method = "vsn", normalize.pa...

...* tkWidgets: The importWizard functionality was added, which provides an Excel style interface for importing data into R. Also the DPExplorer is new in 1.2 - allowing users to explore a BioC data package. The argsWidget widget set will create a GUI for accepting input dynamically. * vsn: vsn can now be used as a normalization method with the affy package. The likelihood function optimization has been streamlined and is faster. There is a new function to produce a diagnostic plot for the variance-mean relationship of microarray data, meanSdPlot. The data returned by vsn is...

How can I efficiently index all choose(m, k) subsets of m items taken k at a time? For example, with (m, k) = (3, 2), the subsets are (1, 2), (1, 3), and (2, 3). I'd like a function something like "index.subsets(subset, k, m)" that would return 1, 2 or 3 for these 3 subsets. Examples: index.subsets(c(1,2), 2, 3) -> 1 index.subsets(c(1,3), 2, 3) -> 2

...ot; "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 the same commands, as above, but the same thing happens. Does anyone have any suggestions? Thanks,...

Hi I'm new to R and have been resisting posting to the list thus far, but I think I've exhausted my work around options. I'm having a few problems with RMySQL and/or it's underlying packages. I'm doing a very simple vsn transformation on large datasets, using RMySQL to retrieve the data for a DB. My first problem was that I could not get the RMySQL package to write back to my DB using the dbWriteTable method. I constructed a data frame with columns corresponding to the table fields, and tried with and with...

...ed] Error 2 This is most unusual - I must have built R from source five or six times going back to 1.5.0 and don't recall any problems like this. Does anyone have any suggestions about where I might look for the source of this problem. In particular, I'm interested in using package 'vsn', whose installation is (I believe) blocked by this problem. I downloaded the source from CRAN this afternoon, choosing the version 2.1.0 'stable' code. I don't have sysadmin privileges on the build machine, but this has never been a problem before - I just pass --prefix=$HOME t...

...sid, residuals, weights The preprocess command in the affyPLM package needs an affybatch object to work with. our preprocess is as such definiert: preprocess <- function(x,...) UseMethod("preprocessExpData") preprocessExpData.expData <- function(data){ require("vsn") data <- list(ExpressionSet=vsnrma(data$AffyBatch), baseDir=data$baseDir,experimentName=data$experimentName, pData=pData(data$AffyBatch)) class(data) <- c("expSet","list") return(data) } when using the workflow we have and coming to the point of preproce...

Is there any documentation on what kind of SPSS file can and cannot be read by read.spss? Alternatively, how can one modify or "clean" an SPSS file to make it readable by read.spss? What properties must a *.sav file before read.spss can read it? The file in this example is 270KB, with 5 rows and 173 columns. I have no trouble reading larger files with read.spss, so it's not

Hola! I am programming a class (S3) "symarray" for storing the results of functions symmetric in its k arguments. Intended use is for association indices for more than two variables, for instance coresistivity against antibiotics. There is one programming problem I haven't solved, making an inverse of the index function indx() --- se code below. It could for instance return the

...splice variants. It can extract simple splice-variant information in XML format. This is demonstrated by the connectivity to an existing database of putative splice variants. The package can also integrate easily with the results obtained from the package 'matchprobes'. --- vsn: Two new functions were added 'sagmbSimulateData' and 'sagmbAssess' to quantitatively verify finite sample properties and outlier robustness of the parameter estimation in vsn(). -- TOOLS: The released packages include tools which facilitate: * annotation (AnnBuilder,...

...splice variants. It can extract simple splice-variant information in XML format. This is demonstrated by the connectivity to an existing database of putative splice variants. The package can also integrate easily with the results obtained from the package 'matchprobes'. --- vsn: Two new functions were added 'sagmbSimulateData' and 'sagmbAssess' to quantitatively verify finite sample properties and outlier robustness of the parameter estimation in vsn(). -- TOOLS: The released packages include tools which facilitate: * annotation (AnnBuilder,...

...s: ******* BEGIN SNIPPET ******* get_stats <- function(t) { cnfac <- factor(t$cnset); mu <- as.list(by(t$snr, cnfac, mean)); tvar <- as.list(by(t$snr, cnfac, var)); t <- list(mu=mu, var=tvar); } vn <- read.table('vn.csv', sep=','); vn_stats <- get_stats(vn); vsn <- read.table('vsn.csv', sep=','); vsn_stats <- get_stats(vsn); snrs <- as.numeric(names(vn_stats$mu)) matplot(snrs, cbind(vn_stats$mu, vsn_stats$mu)); windows(); matplot(snrs, cbind(vn_stats$var, vsn_stats$var)); ******* END SNIPPET ******* Appreciate any helpful hint...

I'm just dumping all I got in here, after initial feedback we can see how to organize todo's around it. tl;dr: * Does not upgrade cleanly from 4.8 packages, so we have to prevent this from entering testing until we fix that. * Live migration is broken, explodes with memory allocation errors. ---- >8 ---- 1. Build packages * I have built salsa/master using pbuilder targeting sid.

Is there a document available that gives a clear description of the layout of data in a version 2 .RDA file. I have a free program (http://www.vsn-intl.com/genstat/downloads/datald.htm) (Windows/Linux/Sun MOTIF exes available) that reads and writes a wide range of file formats, and have been requested by my users to add R to this. It already does S+. Regards, David _________________________________________________________ Dr David Baird, B...

Dear who may concern, I am sending you this email to ask if I could have someone help me to write this script I am interested in. I am requesting the script for performing variance-stabilizing normalizations on the R language. Could you please help me on that? If I am asking a wrong person, could you please tell me the right email address I should contact? Appreciated! Thanks! Regards Ruijuan