similar to: scaling data for microarray

Hi: I have clustered microarray gene expression data and trying to map between microarray probe, gene, pathway, gene ontology, and homology for a set of (affy) microarray probes. Is there any package in R which facilitates this? I am looking at bioconductor, but till now could not find a solution. A link to some worked example would be appreciated. Thanks and regards. John [[alternative HTML

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3rd Millennium is announcing the release of its award winning Array Repository and Data Analysis System (ARDAS) version 2. ARDAS is a web-enabled enterprise software system that provides a complete and fully integrated solution to microarray data acquisition, management, and analysis. ARDAS includes three main modules: 1- A Laboratory Information Management System (LIMS) 2- A repository and data

Hey So sorry to be a total newbie, but i'm just finding my feet with R. I heard on the grapevine i could recreate a scanned microarray image, or at least get a good graphic of it from a just a data file. I have .txt files for illumina beadarrays but no images cos the service we used didn't send them. The 'beadarray' package seems to require TIFFs to get the graphic output. Does

Hi, concerning my earlier mail, maybe someone has noted from the variable names that I try to analyse mircoarrary experiments. Does anybody know of a R-implementation of the two-step mixed-model normalization procedure proposed by Wolfinger et al. (2001) J. Comput. Biol. 8:625-637? That would be great, best, joerg

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]]

Hi. I'm running the latest Samba 4.18 on our dc (Linux - Rocky 8.8), and the clients are running the latest 4.17 (Linux - Rocky 8.8) to be upgraded to 4.18 soon. I've noticed an issue for awhile that is really quite strange and wonder if anyone has any thoughts on this. Samba/Kerberos auth has been setup and working for quite a long time, and I don't think the configuration of

On Thu, 19 Oct 2023 15:34:46 -0400 Jason Keltz via samba <samba at lists.samba.org> wrote: > Hi. > > I'm running the latest Samba 4.18 on our dc (Linux - Rocky 8.8), and > the clients are running the latest 4.17 (Linux - Rocky 8.8) to be > upgraded to 4.18 soon. > > I've noticed an issue for awhile that is really quite strange and > wonder if anyone has any

3rd Millennium is announcing the release of its award winning Array Repository and Data Analysis System (ARDAS) version 2. ARDAS is a web-enabled enterprise software system that provides a complete and fully integrated solution to microarray data acquisition, management, and analysis. ARDAS includes three main modules: 1- A Laboratory Information Management System (LIMS) 2- A repository and data

hi all i started recently using R and i found myself stuck when i try to analyze microarray data. i use the "affy" package to obtain the intensities of the probes, i have two CTRs and two treated. HG.U133A.Experiment1.CEL HG.U133A.Experiment2.CEL HG.U133A_Control1.CEL HG.U133A_Control2.CEL 1007_s_at 2156.23115 467.75615 364.60615 362.11865

Full_Name: Eric Libby Version: 2.1.1 OS: OS Tiger Submission from: (NULL) (65.93.158.117) I am trying to analyze microarray data of 42 human arrays. I typed in the following instructions: library(affy) Data <-ReadAffy() eset <- expresso(Data, normalize.method="invariantset", bg.correct=FALSE, pmcorrect.method="pmonly",summary.method="liwong") And I get some

On 7/28/2020 4:11 PM, Jason Keltz wrote: > > On 7/28/2020 3:59 PM, Jason Keltz via samba wrote: >> I'm experimenting with smb + winbind. >> >> My host is joined to AD and I can login to my host fine using my AD >> credentials via SSH.?? The only issue is that I don't get a Kerberos >> ticket generated. >> >> In

Hi Steven- Nice, but will this not break Windows? From an initial glance over your patch, it seems to assume the existence of mmap() in some form or other. Alistair On 8 Aug 2010, at 03:05, Steven Noonan wrote: > Hi folks, > > I've been doing work on memory reduction in Unladen Swallow, and > during testing, LiveRanges seemed to be consuming one of the largest > chunks of

Hi folks, I've been doing work on memory reduction in Unladen Swallow, and during testing, LiveRanges seemed to be consuming one of the largest chunks of memory. I wrote a replacement allocator for use by BumpPtrAllocator which uses mmap()/munmap() in place of malloc()/free(). It has worked flawlessly in testing, and reduces memory usage quite nicely in Unladen Swallow. The code is available

Hi, I am following the protocol outlined here for analysis of single channel Agilent microarray data: http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma I keep getting the following error message when using Limma's read.maimages function to load my data into an RGList object: Error in RG[[a]][, i] <- obj[, columns[[a]]] : number of

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

Hi all, I am currently doing a consistency analysis using an lmer model and trying to use parametric bootstrapping for the confidence intervals. My model is like this: model<-lmer(y~A+B+(1|C/D)+(1|E),binomial) where E is the individual level for consistency analysis, A-D are other fixed and random effects that I have to control for. Following Nakagawa and Scheilzeth I can work out the

Dear list, I am trying to perform a significance analysis of a microarray experiment with survival data using the {samr} package. I have a matrix containing my data which has 17816 rows corresponding to genes, and 286 columns corresponding to samples. The name of this matrix is data.matrix2. Some of the first values of this matrix are: data.matrix2[1:3,1:5] GSM36777 GSM36778 GSM36779

Hi, May be this helps: ?set.seed(24) ?mydata4<- as.data.frame(matrix(sample(1:100,10*38,replace=TRUE),ncol=38)) ?dim(mydata4) #[1] 10 38 ?library(matrixStats) res<-do.call(cbind,lapply(1:400, function(i) {permutation<-sample(mydata4); (rowMeans(permutation[,1:27])-rowMeans(permutation[,28:38]))/(rowSds(permutation[,1:27])+rowSds(permutation[,28:38]))} )) ?dim(res) #[1]? 10 400 A.K.

Dear maintainer, I used bioconductor package, pdInfoBuilder, to make a microarray platform annotation package. I named this package, pd.pdinfo.gpl11164.ndf.txt. This "self-made package" is to be used with oligo package. Prior to using oligo package, I need to install the annotation package, pd.pdinfo.gpl11164.ndf.txt, and cannot just copy it to the library tree. I tried using the