similar to: Correlation analysis for an exon array

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

Dear All, Thank you kindly for such detailed replies. I was looking to overlay data using algorithms so that i am able to tell which genes are differentially expressed due to changes in copy number. I did a pubmed search and found only 7 literature pieces all of which use in-house algorithms. I am yet to explore Gviz since it wouldn't work on R 2.14, would try it after upgrading to R 2.15.

Dear Bioc and R List Users, I am having trouble analysing illumine data generated from BeadScan. I have .idat files and 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

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

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 downregulated. This is not true for my data since toptable output shows Log fold change greater than > 2. I am

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

dear members, i would like to write a variable in a plot title (main="") but i don't know the right syntax:(...i tried a lot of different ways without success. here my example: y=30 z=33 for (i in 10:length(tissue)) { png(filename = tissues[i], width = 1024, height = 768, pointsize = 12, bg = "white") gene.graph("ENSG00000115252", rma.affy, gps=list(1:3,

Hello, I've meanwhile got onechannelGUI running (my OS is windows). I'm trying to use it for the analysis of human exon arrays. I was able to load cel files and run them through affymetrix power tools, to obtain normalized affy data. My next step was trying to find differentially spliced exons. The menu offers to calculate either Midas or splice index scores. However, when I try to use

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HI, this is my problem I want to subset this file df, using only unique df$exon printing the line once even if df$exon appear several times: unique(df$exon) will show me the unique exons If I try to print only the unique exon lines with df[unique(df$exon),] -this doesn't print only the unique ones :( could you help? thanks Nat exon size chr start

Hi everyone, I am trying to find a way to filter a table; If I am given for example the following table: > head(intra) chr miRNA start end strand ACC hsa_ID region region_start region_end gene_id transcrip_id 1 chr1 miRNA 1102484 1102578 + ACC="MI0000342"; ID="hsa-mir-200b"; exon 1102484 1102578 NR_029639 NR_029639 2 chr1

Hi, I am given the following table: > head(hsa_refseq) chr genome region start stop nu strand nu.1 nu.2 gene_id 1 chr1 hg19_refGene CDS 67000042 67000051 0 + 0 gene_id NM_032291 2 chr1 hg19_refGene exon 66999825 67000051 0 + . gene_id NM_032291 3 chr1 hg19_refGene CDS 67091530 67091593 0 + 2 gene_id NM_032291 4 chr1 hg19_refGene exon

I'm working on Human Exon Array 1.0 ST. I'm getting normalized data fine but I'm running into problems with QC. QCReport gives me the following error: > load(file= "huex10stv2cdf.rda") > exon.data at cdfName <- "huex10stv2cdf" > QCReport(exon.data, file = "QCReport.pdf") Error in as.vector(ans[[i]][, i.probes]) : subscript out of

Hello, I am new to R and still feeling my way thru it. I am trying to plot the values from this file below on the X-axis of a plot. I have attached the graph to the email...the one i am trying to recreate. Exon start end 5'UTR 22540060 22540121 1 22540122 22540140 2 22540303 22540493 3 22541552 22541565 4 22542373 22542519 5 22544265 22544432 3'UTR 22544433 22544856 I would like to

On Thu, Mar 24, 2016 at 6:35 PM, Duncan P. N. Exon Smith < dexonsmith at apple.com> wrote: > > > On 2016-Mar-24, at 12:58, Teresa Johnson <tejohnson at google.com> wrote: > > > > > > > > On Thu, Mar 24, 2016 at 6:35 AM, Duncan Exon Smith <dexonsmith at apple.com> > wrote: > > > > > > On Mar 24, 2016, at 6:22 AM, Teresa

Hi all, In short: I'm running ddply on an admittedly (somehow) large data.frame (not that large). It runs fine until it finishes and gets to the "collating" part where all subsets of my data.frame have been summarized and they are being reassembled into the final summary data.frame (sorry, don't know the correct plyr terminology). During collation, my R workspace RAM usage goes

> On 2016-Mar-24, at 12:58, Teresa Johnson <tejohnson at google.com> wrote: > > > > On Thu, Mar 24, 2016 at 6:35 AM, Duncan Exon Smith <dexonsmith at apple.com> wrote: > > > On Mar 24, 2016, at 6:22 AM, Teresa Johnson <tejohnson at google.com> wrote: > >> >> >> On Wed, Mar 23, 2016 at 11:06 PM, Duncan P. N. Exon Smith

Hi, Prof Duncan I am sorry to report to a wrong place. But I am lucky to meet you by chance, right? Thanks first ^^ 1. The variable y1 is an array get from Perl, each element is from a database (the type should be numeric). Here is the code for that. $query = qq{ select exonCount, count(hsEnsGene) as geneCount from countTop1000ks group by exonCount order by exonCount;

Hi, Prof Duncan I am sorry to report to a wrong place. But I am lucky to meet you by chance, right? Thanks first ^^ 1. The variable y1 is an array get from Perl, each element is from a database (the type should be numeric). Here is the code for that. $query = qq{ select exonCount, count(hsEnsGene) as geneCount from countTop1000ks group by exonCount order by exonCount;

On Thu, Mar 24, 2016 at 6:35 AM, Duncan Exon Smith <dexonsmith at apple.com> wrote: > > > On Mar 24, 2016, at 6:22 AM, Teresa Johnson <tejohnson at google.com> wrote: > > > > On Wed, Mar 23, 2016 at 11:06 PM, Duncan P. N. Exon Smith < > dexonsmith at apple.com> wrote: > >> >> > On 2016-Mar-22, at 19:28, Duncan P. N. Exon Smith via