[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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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 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 error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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), paste, collapse=",
>"), +DESC=sapply(contents(hgu133plus2GENENAME), paste, collapse=", "));
or
>ID <- featureNames(eset)
>Symbol <- getSYMBOL(ID, "hgu133plus2.db")
>tmp <- data.frame(ID=ID, Symbol=Symbol, Name=Name, Ensembl=Ensembl,
>stringsAsFactors=F)
>tmp[tmp=="NA"] <- NA # The stringsAsFactors makes "NA" characters
>fData(eset.norm) <- tmp
Regards,
Ekta
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Peter Langfelder
Sent: 03 April 2012 23:00
To: email mail
Cc: r-help@r-project.org
Subject: Re: [R] how to map microarray probe to gene, homology
On Tue, Apr 3, 2012 at 7:21 AM, email mail wrote:
> 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.
Yes, Bioconductor has annotation packages for microarray chips plus
other packages for connecting gene identifiers to (for example) gene
ontologies.
For example, the package hgu133plus2.db contains annotations for the
U133 plus 2 chip and you can use to map affy probe IDs to gene
symbols, IDs, GO terms etc. Install the package, load it, then type
ls("package:hgu133plus2.db")
and look at the help files for each topic for more details and examples.
The array annotations are chip-specific so you need to choose the
right package for your chip.
Peter
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[R] Read .idat Illumina files in R
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 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 in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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 : +91-80-66628346 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 error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] FW: [BioC] Overlay Gene Expression on SNP (copy number) data
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. Other package - ggbio , work on an input 'Object'. 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: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, Apr 23, 2012 at 6:33 AM, Ekta Jain mailto:ekta_j...@jubilantbiosys.com>> wrote: Hello, Can anyone please suggest any packages in R that can be used to overlay gene expression data on SNP (affymetrix) copy number ? Hi Ekta, If you mean visually, as Steve suggested, you could try packages like ggbio, Gviz, Rcytoscape.. it depends on how you plan to visualize your data, track-based? circular view? net work? and what format your data are? for example, in ggbio, it depends on what data you are using, you can arrange your data into GRanges manually or just provide data that rtracklayer supported like bed, then just use autoplot, it accepts different objects, like GRanges, IRanges, bamfiles or character... allow some transformation like coverage. For files like bed, it automatically use bar to represent your data and use score as y(you can specify other y). Function tracks() allow you to bind or overlay any graphics produced by ggbio or ggplot2, so you could work from data.frame too, it will help you align your plots after the graphics are produced. For genomic structure, if you want to overlay with your data, try autoplot, TranscriptDb. And if you want to show interaction between genes, you could try either arches in linear view or links in circular view(layout_circle). http://tengfei.github.com/ggbio/ this website is still under development, just to show some possible cases, it will be re-built against R 2.15 and more case studies are coming. HTH Tengfei Another possibility for visual display of several kinds of data is RCytoscape, for which an example can be seen here: http://rcytoscape.systemsbiology.net/versions/current/gallery/TCGA/subnet.TCGA.02.0014.png This portrays 1) gene expression (green: under-expression; red: over-expression) 2) copy number (blue: high, black: low) 3) gene type (node shape: hexagons are kinases, arrows are ligands, diamonds are receptors, circles for everything else) 4) mutation status (not SNPs, but non-synonymous amino acid substitutions) 5) in the context of gene relationships, from KEGG A vignette for a larger version of this network is nearly complete. The Cytoscape network map is created from data and R code. - Paul Hi, On Mon, Apr 23, 2012 at 7:33 AM, Ekta Jain mailto:ekta_j...@jubilantbiosys.com>> wrote: > Hello, > Can anyone please suggest any packages in R that can be used to overlay gene > expression data on SNP (affymetrix) copy number ? I guess you mean visually? If so, I'd suggest skimming through the vignettes of the following packages to see which one might suit you best: * Gviz * ggbio * GenomeGraphs -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact 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 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 error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a!
[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 downregulated. 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) <- levels(fl)
> fit <- lmFit(eset, design)
> cont.matrix <- makeContrasts(DMSO10-Un, DMSO5-Un, levels=design)
> fit2 <- contrasts.fit(fit, cont.matrix)
> fit2 <- eBayes(fit2)
> tTUni<- topTable(fitUni, adjust="fdr", sort.by="B", number=numGenes)
> results <- decideTests(fit2)
> vennDiagram(results,include=c("up","down"),counts.col=c("red","green"))
## ### I get zero genes for upregulation and downregulation #
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 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 error, please
notify the sender and system manager by return email and delete the message and
its attachments and also you are hereby notified that any distribution,
copying, review, retransmission, dissemination or other use of this electronic
transmission or the information contained in it is strictly prohibited. Please
note that any views or opinions presented in this email are solely those of the
author and may not represent those of the Company or bind the Company. Any
commitments made over e-mail are not financially binding on the company unless
accompanied or followed by a valid purchase order. This message has been
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nd is believed to be clean. The Company accepts no liability for any damage
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www.jubl.com
[[alternative HTML version deleted]]
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