search for: hgu133a

Hi, I am wondering how to make a function Fun to make the following work: t0 <- (paste("hgu133a", "ENTREZID", sep="")) xx <- as.list(Fun(t0)) # make it work like xx<-as.list(hgu133aENTREZID) thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Hello, Im trying to combine 3 affybatches (1x hgu133+2 array and 2x hgu133a array) Im useing this script: library(matchprobes) library(affy) library(AnnotationDbi) library(hgu133plus2probe) library(hgu133aprobe) library(hgu133a.db) u133p2 = ReadAffy() # reading hgu133 +2 cel file into affybatch u133a1 = ReadAffy() # reading hgu133a cel file into affybatch u133a2 = ReadAf...

...package that scans namespaces for functions with a certain class attribute. For this I use is.function() and inherits() to inspect each object. An aroma.affymetrix user reported on a problem that boiled down to the following: # source("http://bioconductor.org/biocLite.R"); biocLite("hgu133a.db") > library("hgu133a.db") > is.function(hgu133aPFAM) Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM or PROSITE accessions. > .Internal(inspect(hgu133aPFAM)) > traceback() 3: stop(paste(msg, collapse = ""), call. = FALSE, doma...

...v() > delayedAssign("foo", stop("Hey!"), assign.env = e) > substitute(foo, e) > > delayedAssign("foo", stop("Hey!")) > substitute(foo) Hmm... interesting and odd. Unfortunately, this doesn't seem to help for reaching into the namespace of hgu133a.db and inspecting 'hgu133aPFAM', e.g. > library("hgu133a.db") > substitute(hgu133aPFAM, env=ns) Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM or PROSITE accessions. > evalq(substitute(hgu133aPFAM), envir=ns) Error: hgu133aPFAM is defun...

Hello, I want to use expresso for preprocessing the hgu133a-spikein data from affycompII. But there is an error: > library(affy) > path <- "z:/Microarray/hgu133a-spikein/rawdata" > celFile <- list.celfiles(path=path,full.names=TRUE); > affyBatch <- ReadAffy(filenames=celFile[1:6]); > eset1 <- expresso(affyBatch,b...

...paces for functions with a certain class attribute. > For this I use is.function() and inherits() to inspect each object. > An aroma.affymetrix user reported on a problem that boiled down to the > following: > > # source("http://bioconductor.org/biocLite.R"); biocLite("hgu133a.db") >> library("hgu133a.db") >> is.function(hgu133aPFAM) > Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM > or PROSITE accessions. >> .Internal(inspect(hgu133aPFAM)) > >> traceback() > 3: stop(paste(msg, collapse =...

At first I would like to express the gratitude toward Oosting, J. and James MacDonal for their help solving the previous problem I posted on this forum. Now I have a new problem. I was trying to normalize set of microarray data on HGU133 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(Dat...

...;), assign.env = e) >> substitute(foo, e) >> >> delayedAssign("foo", stop("Hey!")) >> substitute(foo) > Hmm... interesting and odd. > Unfortunately, this doesn't seem to help for reaching into the > namespace of hgu133a.db and inspecting 'hgu133aPFAM', e.g. >> library("hgu133a.db") >> substitute(hgu133aPFAM, env=ns) > Error: hgu133aPFAM is defunct. Please use select() if you need access to PFAM > or PROSITE accessions. >> evalq(substitute(hgu133aPFAM...

...7] Biobase_2.12.2 loaded via a namespace (and not attached): [1] affyio_1.20.0 biomaRt_2.8.1 Biostrings_2.21.6 [4] Category_2.18.0 cluster_1.13.3 gdata_2.7.1 [7] genefilter_1.34.0 gplots_2.10.1 graph_1.30.0 [10] grid_2.13.0 GSEABase_1.14.0 gtools_2.6.2 [13] hgu133a.db_2.5.0 Hmisc_3.8-3 hopach_2.12.0 [16] IRanges_1.11.11 lattice_0.19-23 limma_3.8.3 [19] Matrix_0.9996875-3 mgcv_1.7-5 nlme_3.1-100 [22] oligoClasses_1.14.0 RBGL_1.22.0 RCurl_1.6-10 [25] SNPchip_1.16.0 splines_2.13.0 survival_2.36-5 [28] tools_2.13.0...

...structures graphics The R Graphics Package grDevices The R Graphics Devices and Support for Colours and Fonts grid The Grid Graphics Package GSEABase Gene set enrichment data structures and methods hgu133a Affymetrix Human Genome U133 Set Annotation Data (hgu133a) hgu95av2 Affymetrix Human Genome U95 Set Annotation Data (hgu95av2) hgu95av2.db Affymetrix Human Genome U95 Set annotation data...

...252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] GOstats_2.12.0 Category_2.12.0 multtest_2.2.0 R.utils_1.2.4 R.oo_1.6.5 R.methodsS3_1.0.3 genefilter_1.28.0 [8] hgu133a.db_2.3.5 org.Hs.eg.db_2.3.6 GEOquery_2.8.0 RCurl_1.2-1 bitops_1.0-4.1 biomaRt_2.2.0 affy_1.24.1 [15] int.intact.db_1.1.1 int.geneint.db_1.1.1 PAnnBuilder_1.8.0 RpsiXML_1.6.0 hypergraph_1.18.0 XML_2.6-0 RBGL_1.20.0 [22] ann...

When I try to load cel files (hgu133a) using the ReadAffy() in R 1.8.1 command I get an error message: > x<-ReadAffy() Error: cannot allocate vector of size 102973 Kb Does anybody know what does this error mean and how to overcome it? I have tried to load the same data with R 1.7.1 and it works. There is also no error when I u...

...TIME=English_United States.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" [6] "datasets" "methods" "base" other attached packages: affy affyio Biobase hgu133acdf hgu133a "1.14.0" "1.4.0" "1.14.0" "1.16.0" "1.16.0" ====================================== Benjamin Otto University Hospital Hamburg-Eppendorf Institute For Clinical Chemistry Martinistr. 52 D-20246 Hamburg Tel.: +49 40 42803 1...

...evertheless I want to check my results with an other method. Therefore I look for one and want to ask you, what you suggest. I have 3 different patient groups, only the steady state data, 10/10/13 (total of 33) arrays and the challenge is to classify the groups by the expression of all genes on the hgu133a chip. The named rule-based method found for each group genes, which explain a classification for each sample to one of the groups. Are there packages/method you can suggest? I guess PAMR works not so good for all genes on the chip, right? Would be amazing if you can tell me your opinion. All the...

...only, MM-only, both PM and MM together or PM and MM separately. --- affycomp: New assessment was added: assessSpikeIn2. Examples of new feature: Local slopes are computes and ROC curves divided by overall expression. Also, all functions that work for hgu95a spike in now also work for hgu133a spike in experiment --- annaffy: Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria...

...only, MM-only, both PM and MM together or PM and MM separately. --- affycomp: New assessment was added: assessSpikeIn2. Examples of new feature: Local slopes are computes and ROC curves divided by overall expression. Also, all functions that work for hgu95a spike in now also work for hgu133a spike in experiment --- annaffy: Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria...

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is