[R] CHAID Analysis in R

Dear all, I have been researching on whether there is a package in R that can do CHAID analysis. The CHAID package in R-Forge is not available for windows and thus wondering if at all there is something equivalent in R? Many Thanks, Ekta [[alternative HTML version deleted]] _

[R] LIMMA decideTests result zero from contrast matrix

Dear All, I am using the LIMMA package to create 2 contrasts for my data and then calculating the vennCounts of the decideTests from the contrast.fit to be able to create venn Diagrams. The code works fine but the summary(results) shows zeros for all i.e. no gene were up regulated or downregula

[R] FW: [BioC] Overlay Gene Expression on SNP (copy number) data

ny more help or thoguhts here will be greatly appreciated. Thanks a ton ! -E From: Tengfei Yin [mailto:yinteng...@gmail.com] Sent: 23 April 2012 21:30 To: Ekta Jain Cc: bioconduc...@r-project.org; r-help@r-project.org Subject: Re: [BioC] Overlay Gene Expression on SNP (copy number) data On Mon,

[R] Overlay Gene Expression on SNP (copy number) data

Hello, Can anyone please suggest any packages in R that can be used to overlay gene expression data on SNP (affymetrix) copy number ? Thanks, Ekta Senior Research Associate Bioinformatics Department Jubilant Biosys Pvt Ltd, #96, Industrial Suburb, 2nd Stage Yeshwantpur, Bangalore 560 022 Ph No :

[R] Read .idat Illumina files in R

analysis or do i need to go back to BeadScan and generate .txt files/tiff files ? Appreciate any help here. Many Thanks, Ekta Jain The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the

Re: [R] how to map microarray probe to gene, homology

Hi, You could use the s apply function to create a data frame of the annotation. If hgu133 plus 2.0 is your chip something like the following could be employed >myAnnot <- data.frame(ACCNUM=sapply(contents(hgu133plus2ACCNUM), paste, >collapse=", "), SYMBOL=sapply(contents(hgu133plus2SYMBOL), pas

[R] Correlation analysis for an exon array

Dear All, I have an exon array and did not find any differential gene expression between two samples. I was looking to perform correlation analysis on the same. Can anyone recommend any package that would do this for an affy exon array? Will SAM analysis give me correlated genes? Thanks and reg