search for: affymetrix

I don't know if this is the correct forum to ask the following question; however, when I search the aroma.affymetrix discussion group, it suggested that I should posted the question to r-help. Here it goes. I followed the instructions on aroma.affymetrix trying to install the packages; following are the steps: > install.packages(c("R.oo", "R.utils"), contriburl="http://www.bra...

Hi everyone, My purpose is to read a .CEL file into R. The .CEL file was created from a .CAB by using DTT software found on Affymetrix website I read the .CEL file in R using ReadAffy as follows: > d2=ReadAffy(widget=T) and I complete the fields as required. It does not complain. For example I could find the description: > description(d2) Experimenter name: BB Laboratory: FFL Contact information: Title: Heter URL: www...

I have CEL files from Affymetrix Mouse Array 430_2 and am trying to get the the individual PM intensities (11 per gene) for each sample. I would like to write out this into a tab delimited text file. Where am I stalling? This is what I've done: Change dir(to where CEL files are saved) Data <- ReadAffy() eset <- rma(D...

Hi, I am trying to read in my Affymetrix CEL files (48 files, total ~600 MB) but I keep getting memory errors. Can somebody please help me with this. Or is therea remote server I can send my data to for computation? Any help is much appreciated. Thanks Dr. Tristan Coram Postdoctoral Research Associate Research Plant Pat...

...Can anyone tell me the corresponding command? Thanks, Corinna Here is the result of the command library(): Pakete in Library 'D:/R/R-2.6.0/library': ada Performs boosting algorithms for a binary response affy Methods for Affymetrix Oligonucleotide Arrays affycomp Graphics Toolbox for Assessment of Affymetrix Expression Measures affydata Affymetrix Data for Demonstration Purpose affyio Tools for parsing Affymetrix data files affyPLM Methods...

Hi, Is there a way to turn off the automatic inclusion of "./" at the beginning of a path specified in an \SweaveInput{} instruction? I'd like to create some reusable "template modules" of Sweave code and put them in a standard directory like /Resources/Affymetrix Then the corresponding file that uses one of these would include a command like \SweaveInput{/Resources/Affymetrix/libload.Rnw} If I try that (in R 2.4.0 on either Windows or UNIX), however, I get an error message to the following effect: -------------------------------- Writing to file affyExa...

Is there any package that allow you to perform "MA plot" like graph for Toray microarray data? Unlike Affymetrix CEL file which contain 2 values (R and G), Torray raw data only contain 1 value. MA-plot is Affymetrix specific which usually available for in (limma) package. P. Dubois [[alternative HTML version deleted]]

...irectories during installation? The immediate need I have right now is that untar an archive to inst/testScripts/. The reason why I need this is that a package can only contain pathnames of length <= 100 characters (restriction in the tar file format), and mine are longer than that, e.g. aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20080730,100K,BPN,alleleSpecific.R [115 chars]. See also http://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora/aroma.affymetrix-00check.html . One strategy is to create a local tar file referring to files system/chipTypes...

mogene10stprobeset.db is generated with AnnotationDbi for mouse gene array. I don't find a package that seems generated by AnnotationDbi for exon arrays on the webpage you mentioned. Is it correct? On Tue, Oct 27, 2009 at 7:00 PM, Marc Carlson <mcarlson at fhcrc.org> wrote: > Hi Peng, > > I am not completely clear from your post what you want. ?But most of our > annotation

I am looking for an online (easily accessible) form of the samples of genetic data for those with cancer and those without cancer. Can anyone direct me in the right place? Thanks, Jim [[alternative HTML version deleted]]

Hi List, I'm trying to install aroma.affymetrix, which depend on many packages, affyio is one of them. The task is done on 32-bit Linux without problem. The same task was done on Solaris 9 with R-2.5.1 without problem. Following is the error message when installation affyio. I did try to put a file stdint.h I got from the web in the path, but go...

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

Dear All, There is a question I met when using Affy package in Bioconductor. I asked it in BioC and didn't get any responses. Sorry to post again: Could anyone tell me how to draw a deep-blue Affymetrix image through Image() function in Affy package? The default settings of image() draw me a black-white image and if I modify it to 256 colors, I get a somehow yellowish image. The reason for me to draw a deep-blue one is because I found most of papers display the spotted cDNA microarray image as red...

hi i have a huge matrix and want to split it into 2. with the command %%2. but i get this warning message: *"Error in mmat%%2 : non-numeric argument to binary operator*" here's the bit from my matrix: V1 V2 [1,] "Affymetrix:CompositeSequence:ATH1-121501:244901_at" "2.653" [2,] "Affymetrix:CompositeSequence:ATH1-121501:244902_at" "1.753" -- all the best, Baur [[alternative HTML version deleted]]

Hi, I have 15 CEL files of Affymetrix platform from GEO. Title of experiment is : Ecoli_ASv2 Affymetrix E. coli Antisense Genome Array. I am looking for the package available in R for this array for annotation. I have already tried doing annotation from packages like org.EcK12.eg.db but I don't got the success. Is any other pa...

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 chi...

...regards Desmond Campbell Room C0.29, SGDP Centre Institute of Psychiatry, De Crespigny Park, London SE5 8AF Tel: +44 (0) 20 7848 0236 Fax: +44 (0) 20 7848 0866 Announcing the 7th MRC SGDP SUMMER SCHOOL 17 - 21 July 2006 with courses in a) twin model fitting, Mx b) gene expression and microarrays (Affymetrix) c) linkage, association and allied methods See http://sgdp.iop.kcl.ac.uk/summerschool/

...ion, I have set --max-mem-size=2G but I run out of memory somewhere around 500Mb (which is why I am trying to find out how much memory is allocated). I don't have any other programs open, so I should certainly be able to address more memory than that. Any ideas? TIA Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

...ignment? Is it possible to test if this is a delayed assigned or not? BACKGROUND: The background to this is where I have a function in the R.oo 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...

Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdiff medianpolish mas There are many options within each method. I would appreciate a hint on the best combination. Thank yo...