search for: mas5

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: ...

Dear all, I was trying to normalize a subset of affy data those transcribe are either P or M (called pm_filter). I am able to normalize pm_filter subset by using RMA method, however MAS5 is not working. For RMA method, I used the following commend: est<-rma(affydata, subset=pm_filter). Could any help me; how do I do this by using MAS5 method? Regards, Anup Som -- Dr. Anup Som, Ph.D. Institute for Biostatistics and Informatics in Medicine and Ageing Research University of R...

Hi.... I have a question about how to increase my memory size, could someone answer it for me?? I am using Bioconductor in R to calculate gene expression values with mas5, dchip, and mas4. I have only 18 samples, all from Affymetrix U133A Plus 2 arrays, which has ~54,000 genes. My machine equipments are: CPU P4 3.0GHz, and 1GM RAM. Somehow when I was running mas5 in R, it always showed the error message: "Cannot allocate vector of size 211702 Kb." I believ...

Hi all.. I'm very new R, and i'm analyzing microarray data using Bioconductor.. Recently i was given 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...

...how to fix this problem? I was able to run the same data set with gcc-compiled R2.1.1 and BioConductor 1.6 successfully. Here is the code that I ran, if it helps to diagnose the problems. library(simpleaffy); library(affy); ampli.data <- ReadAffy() # normalize the data using call.exprs and mas5 ampli.eset <- call.exprs(ampli.data, "mas5") # see what data is stored in ampli.eset at description@preprocssing names(ampli.eset at description@preprocessing) # acess each piece of information within ampli.eset at description@preprocessing scale factors ampli.eset at description@pr...

...133 paltform. I put all 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 va...

.... 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 Affymetrix's then in previous releases, and now includes a function mas5() to make it easier for a user to obtain these results. * affycomp: A new package that serves as a graphics toolbox for the assessment of Affymetrix expression measures. * AnnBuilder: DB support is no longer required. ABPkgBuilder now provides a signle API for building of data packa...