For eg look **at the structure** of ff object you created using read.table.ffdf(). normalize.quantiles generating incorrect output Hi Jeffrey, I think this is because you are passing 'normalize.quantiles' a matrix of integers, ... segmentation fault with using normalize.quantiles(), affy library Hi, I am using R-1.8.1.alpha with affy_1.4.1 in Unix system, and now experiencing "Segmentatio... Some of these ... have a peek at this web-site

Hello, I am trying to do background correction/ quantile normalization on a .txt file of express... normalize.quantiles generating incorrect output Hello everybody, I'm using the normalize.quantiles function from the "affy" package version 1.3.... How To Perform Basic Multiple Sequence Alignments In R? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi Radhika, On Jun 30, 2009, at 5:34 PM, Radhika Ambatipudi wrote: > Hi > > https://stat.ethz.ch/pipermail/bioconductor/2009-June/028384.html

I run out o... The "normalize.quantiles" function is in the preprocessCore library, which needs to be loaded first, like so: ===== R> library(preprocessCore) R> ... I don't have resources to such large computations. featureData: none experimentData: use'experiment...

ADD REPLY • link written 3.4 years ago by Devon Ryan ♦ 59k Got it from GEO database as "Dataset SOFT file". SciClone not numeric error I tried to use sciClone on test data prior to applying any script on my actual patient database, ... Binding several large matrices by column I truly know that 'large matrix issue' is a recurrent topic here, but I would like to explain min... Tukeys'S Hsd After Anova Using R The dataset has 1000 genes and contains 24 samples with two mouse strains tested (129 and B6) and...

Please help me to pinpoint the error..? I joinded them in a matrix in which every row is a vect... I am trying to normalize 4 sample sets of CEL data generated by using Tiling array. ADD REPLY • link written 3.4 years ago by Devon Ryan ♦ 59k library(GEOquery) # get the ExpressionSet, usually normalized already eset = getGEO("GSE32394")[[1]] # get the .CEL files getGEOSuppFiles("GSE32394") ADD

using regular expression matching: preprocessCore::normalize.quantiles Quantile Normalization preprocessCore::normalize.quantiles.in.blocks Quantile Normalization carried out separately within blocks of rows preprocessCore::normalize.quantiles.robust Robust Quantile Normalization preprocessCore::normalize.quantiles.use.target Quantile Normalization using a specified target distribution vector Type I h... normalize.quantiles function not **recognized by R Hi I** am very new to R. Ambatipudi, you find the function (normalize.quantiles) in the affy packgae.

It is possible to dig out these internal functions and use them, even though it might not be recommended. http://grokbase.com/t/r/bioconductor/096yy5t7np/bioc-normalize-quantiles-function-not-recognized-by-r an error in normalize.quantiles {preprocessCore} function? I joinded them in a matrix in which every row is a vector, with the command: TOT=do.call(rbind,list) in which TOT is the final matrix and list is a list with the 4 Normalization of microarray data?

Powered by Biostar version 2.2.0 Traffic: 70 users visited in the last hour sign up / log in • about • faq • rss Ask Question Latest News Jobs Tutorials Check This Out Hi all, I am using normalize.quantiles in package preprocessCore to deal with my data now, and... Similar posts • Search » normalize.quantiles function not recognized by R Hi R. Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

How To Analyze These Biological Data? Would you... Similar posts • Search » Bioconductor R And Input File Issue I'm using Gviz library from bioconductor. Source Ambatipudi reply Tweet Search Discussions Search All Groups bioconductor 2 responses Oldest Nested Steve Lianoglou Hi Radhika, The "normalize.quantiles" function is in the preprocessCore library, which needs to be loaded first,

normalize.quantiles function not recognized by R Hi R. Updated Affy: Readaffy Has Changed And Breaks My Pipeline! Error using impute.knn function Dear List, After quantile normalizing some Agilent microarray data I end up with a data matrix c...

LiftOver in R (error) I am trying to use the LiftOver function in `rtracklayer` package but I am getting one error, thi... Nevertheless, my data is in the data.frame format, as I have read my expression data from a .txt file. Can somebody pleasehelp.- R. I am running R 1.6.2 on SUSE Linux 8...

I have been following some i... Memory problems with normalize.AffyBatch.quantiles There appears to be a problem with this function, in particular the C code (qnorm_c). There are sort of 2 replicat... http://gsbook.org/error-could/error-could-not-find-function-paste0.php You could also make a density plot of the intensities, and it'll show whether the data has been normalized or not.

df <-read.delim2(file="del.txt", header=T, sep=" ", stringsAsFactors = F) df$sample1=as.numeric(df$sample1) df$sample2=as.numeric(df$sample2) df$sample3=as.numeric(df$sample3) ############# ##Use davetang code ########### source("quantile.r") quantile_normalisation(df) 3) In addition, I ran following code. Can somebody > please > help. Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy. normalize.quantiles generating incorrect output Hi Jeffrey, I think this is because you are passing 'normalize.quantiles' a matrix of integers, ...

The affy package does have a function normalize.quantiles() but it seems to be inaccessible directly (booooring!). Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the Bioconductor mailing list sign up / log in • about • Please, if you ha... I am examining data from a 2D gel experiment, but my question is about a broader issue of ...

R/Bioconductor: Applying Limma Functions To A Matrix. about • faq • rss Community Log In Sign Up Add New Post Question: Quantile normalization in huge matrices 0 14 months ago by yogacacarolom • 40 Brazil yogacacarolom • 40 I think I have loaded all required packages > but when I call normalize.quantiles function in R, I get an error message : > Error: could not find function "normalize.quantiles". I did this once, if you want I can try to find it for you.

General normalization problem that's *similar* to microarrays. normalize.quantiles generating incorrect output Hello everybody, I'm using the normalize.quantiles function from the "affy" package version 1.3.... Secondary, if the file IS from an Affymetrix platform, and it's in .txt, there is a good chance that it has been normalized already, because of above mentioned binary file.