search for: justrma

I am trying to preprocess a large dataset of affymetrix data. Creating an affybatch is not possible with the computer I am running it on, so I have used the justRMA command to run RMA. I have read the affy document describing the justRMA command and the help documentation but I am unclear as to whether this command uses median polish after normalization. I assume this is the case but would like to be sure before proceeding. Could someone clear up this confu...

Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the directory of these .cel files. I don't know how to give the path for al...

Dear R-help Hi, I'm Won. I try to do microarray normalization by R. I use justRMA function within affy package, got error about segment fault. I don't know why it happen. I attached error below. Please help me. Thank you. Cheers, Won ======================= OS : Redhat linux Cpu : intel xeon X5570 Memory : 26Gb & OS : Ubuntu Cpu : intel q6600 Memory : 8Gb =====...

...see it, there are no restraints on the amount of memory that R can use imposed by this particular OS build. When I type in the 'ulimit' command at the command line the response is 'unlimited'. Here is the problem: I have uploaded and normalized 48 ATH1 microarray slides using the justRMA function. >library("affy") >setwd("/Data/cel") >Data<-justRMA() The next step in my analysis is to calculate a distance matrix for my dataset using bioDist package. This is where I get my error. >library("bioDist") >x<-cor.dist(exprs(Data))...

Hello. By way of background, I am running out of memory when attempting to normalize the data from 160 affymetrix microarrays using justRMA (from the affy package). This is despite making 6 gigabytes of swap space available on our sgi irix machine (which has 2 gigabytes of ram). I have seen in various discussions statements such as "you will need at least 6 gigabytes of memory to normalize that many chips", but my question...

Hello! When I use the functions rma() or justrma() in the Bioconductor affy package, the standard errors for the expression estimates computed by the function se.exprs() is a matrix of NA's. I am wondering if any of you have encountered this problem and if there is a solution. Any help would be appreciated. Thanks, Karthik. [[alternative...

How can I get a single backslash in a character string? My goal is to escape dots in a string that will be used as a regular expression. I thought I could do it this way: gsub(".", "\\.", x) Unfortunately, "\\" does not represent a literal backslash as I expected, but rather a pair of backslashes: > "\\." [1] "\\." > "\\" [1]

I am trying to work with 75 affymetrix U133plus2 chips and am running into memory allocation errors when trying to merge or convert probe level data to expression values. I keep getting - Error: cannot allocate vector of size 561011 Kb and that is simply with a data subset. Is there a way around this limitation? -- Rodney A. Staggs Cancer Center Informatics Shared Resource 425 Delaware St S.E.

Dear R-mailing list Hope you can help me. I am using R for windows to analyze my 107 HGU133Plus2.0 chips, however, R chrash when I try to use ReadAffy(). I want to buy a computer that can handle all these arrays, do you know how big a computer I need to buy? Best, Skov, Denmark [[alternative HTML version deleted]]

...==== * All packages from the 1.1 release are included. All current bug fixes have been applied, and most have been upgraded and provide enhanced functionality. * affy: The affy package now provides for the automatic downloads of necessary CDF packages. There is also a new function, justRMA() which will use less system resources if one just wants RMA vs. using ReadAffy() and then rma/expresso - this will solve some users' problem when they do not have enough memory for working with the full method. The package's implementation of MAS 5.0 now agrees better with Affymetri...

Hi, I am running R 2.0.1.1. on Windows. It is a Dell Dimension with a 3.2 Ghz Processor and 4Gb RAM. When using the ReadAffy() function to read in 97 arrays, I get the below error messages: Error: cannot allocate vector of size 393529 Reached total allocation of 1024Mb: see help(memory.size) When I use the comman "memory.limit(size=4000)" to increase the memory size to the

...ionality. -- 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...

...ionality. -- 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...