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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 : +91-80-66628346 The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and...

...d JPEG images. I realise that i need bead-level summary data to be able to begin quality control followed by normalization. Is there a way i can read .idat files for expression 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 person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message...

...bject'. I am not able to figure out what to provide as object - gene expression data matrix as whole and or SNP log2 normalised ratios? Any more help or thoguhts here will be greatly appreciated. Thanks a ton ! -E From: Tengfei Yin [mailto:yintengfei@gmail.com] Sent: 23 April 2012 21:30 To: Ekta Jain Cc: bioconductor@r-project.org; r-help@r-project.org Subject: Re: [BioC] Overlay Gene Expression on SNP (copy number) data On Mon, Apr 23, 2012 at 6:33 AM, Ekta Jain <Ekta_Jain@jubilantbiosys.com<mailto:Ekta_Jain@jubilantbiosys.com>> wrote: Hello, Can anyone please suggest any pa...

...r 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 regards, Ekta 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 person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in e...

...nregulated. This is not true for my data since toptable output shows Log fold change greater than > 2. I am certain it is a small glitch somewhere at my end that i get zero counts for my summary(decideTests). Please find below my code and i would really appreciate any help here at all. Thanks, Ekta ## R Script ### > numGenes <- nrow(eset) > library(limma) > samples <- c("Un","Un","DMSO10","DMSO10","DMSO5","DMSO5"); > fl <- as.factor(samples) > design <- model.matrix(~ 0+ fl) > colnames(design) <- leve...

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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