search for: mas5cal

...en microarray data to analyze. The problem is whenever i run MAS5 presence calls algorithm, it throws an error saying NA/NaN/Inf in foreign function. How do i remove such NA/NaN/Inf's ?? I tried na.omit(dataframe) but stil problem exists. dimension of matrix (data) is 35556 7. > data.mas5calls=mas5calls(data) Getting probe level data... Computing p-values Error in FUN(1:6[[1L]], ...) : NA/NaN/Inf in foreign function call (arg 2) Thank you. -- ****************************************************************** Anand M.T School of Biotechnology (Bio-Informatics), International Instit...

Hi!I'm doing a little data importing from .cel files, > setwd("/home/mandova/celfiles") > mydata<-ReadAffy() Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : unused argument(s) (extended = TRUE) Then I tried > filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="") >

Hello everybody, I am trying to use mas5 to normalize some array data and using mas5 and mas5calls. But I received these warning message. If anybody can explain the problem I would really appreciate that. Thanks in advance. background correction: mas PM/MM correction : mas expression values: mas background correcting...Warning message: 'loadURL' is deprecated. Use 'load(url())'...

...-I/usr/share/R/include -fpic -g -O2 -std=gnu99 -c chipbackground.c -o chipbackground.o gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -std=gnu99 -c getall_locations.c -o getall_locations.o gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -std=gnu99 -c mas5calls.c -o mas5calls.o gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -std=gnu99 -c qnorm.c -o qnorm.o gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -std=gnu99 -c rma2.c -o rma2.o gcc -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -std=gnu9...

...l the HGU133A platform chips in one directory and all the other HGU133B chips on another directory. When I tried to normalized them using same script HGU133A data worked fine but got error for HGU133B platform data. The code is library(affy) Data <- ReadAffy() eset <- mas5(Data) Calls <-mas5calls(Data) The errors I got are: background correction: mas PM/MM correction : mas expression values: mas background correcting...Warning message: cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/CRANrepository does not seem to have a valid repository, skipping...

...- NEW PACKAGES AND MAJOR UPGRADES FOR RELEASE 1.3 -- The following is an overview of the most important changes, additions, and upgrades: --- affy There have been many improvements to the affy package. There were big speed and memory improvement of ReadAffy, read.affybatch, justRMA. A mas5calls method was added to get Affymetrix's P/M/A calls. Cel and Cdf classes are no longer supported. Function, read.celfile and other Cel related methods and functions removed. Most Cdf related functions have moved to the makecdfenv package. Function read.probematrix added. It reads C...

...- NEW PACKAGES AND MAJOR UPGRADES FOR RELEASE 1.3 -- The following is an overview of the most important changes, additions, and upgrades: --- affy There have been many improvements to the affy package. There were big speed and memory improvement of ReadAffy, read.affybatch, justRMA. A mas5calls method was added to get Affymetrix's P/M/A calls. Cel and Cdf classes are no longer supported. Function, read.celfile and other Cel related methods and functions removed. Most Cdf related functions have moved to the makecdfenv package. Function read.probematrix added. It reads C...