Tag: ReadAffy

using RMA normalized microarray in Limma

using RMA normalized microarray in Limma 0 Hi, i downloaded raw.tar file containing .CEL microarray data from GEO database. and then i use affy() package in R to extracted .CEL file and normalized with RMA(). Can i use this expression data to put in Limma? or it is better to…

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“, cdfname, object ‘cdf’ not found

Hello, I would like your suggestions for this error with rma() function, for analysing microRNA-affymetrix data. I downloaded the package cdf (miRNA-4_0-st-v1_CDF) (provided below), created the package with make.cdf.package, installed it with R CMD INSTALL. library(makecdfenv) make.cdf.package(filename = “miRNA-4_0-st-v1.cdf”, packagename = “miRNA-4_0-st-v1.cdf”, cdf.path = “./miRNA_4_0_CDF/”, package.path= “/shared/home/mkondili/Tools_Packages/”, compress = FALSE,…

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Error in getCdfInfo(object) :

Error in getCdfInfo(object) : 1 @bca66a4b Last seen 1 hour ago Japan Hi I wanted to do a rma analysis for a affymetrix microarray data. but I got a problem. Code should be placed in three backticks as shown below setwd(“~/Downloads/GSE24184_RAW/”) library(affy) library(makecdfenv) data = ReadAffy() data and I got…

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Analysing Microarray Data In Bioconductor

I was thinking about creating a tutorial on how to do a simple microarray analysis in Bioconductor. But, I realized this has already been done quite nicely at the Bioinformatics Knowledgeblog. Their first tutorial on the subject covers installation of necessary packages, downloading of cel files, describing the experiment, loading…

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Error in ReadAffy function

Error in ReadAffy function 0 I want to do a microarray analysis so I got a tar file from the GEO. When I want to read it by ReadAffy() function I get the error below: library(affy) dataset<-ReadAffy(compress=T, celfile.path = “GSE129166_RAW .tar”) Error in AllButCelsForReadAffy(…, filenames = filenames, widget = widget,…

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