Tools for Combining Affy and aCGH data
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Tarun Nayar ▴ 190
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@sean-davis-490
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Tarun Nayar wrote: > Hi, > > Are there any tools out there to combine/ compare Affy gene expression > and aCGH data? A collaborator has 12 aCGH expts and 12 affy expression > chips from the same biological samples. He's interested in seeing if > regions of CN alteration correspond to differences in gene expression. > We've taken a stab at writing our own program for this, now I'm > wondering if there are any pre-made tools to do the same. > I don't know of R/bioc packages for doing this directly, but some version of correlation between CGH measurements and gene expression measures is probably useful. You can use standard R commands to do this. Within any region of amplification, note that there will likely be only a portion (of unknown quantity) of gene expression that is correlated with copy number. Sean
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Hi Tarun, I am currently developping an R package to calculate correlations between copy number and expression measurements. Here are its main features: - Data pre-processing: an unambiguous mapping between genome and transcriptome probes according to their position on the genome. Missing DNA copy numbers are inferred by taking advantage of the consistency of the copy number signal along the genome. - Statistical data analysis: for each probe, a correlation coefficient between DNA copy number and expression data is calculated, as well as an associated p-value. These p-values are then adjusted for multiple comparisons (FDR or FWER). - Data visualisation and interpretation: correlation coefficients and associated significances can be plotted along the genome together with cytobands; results can be exported as csv files. As Sean mentions, our analyses show that only a subset of genes within a region of copy number amplification or deletion have their expression levels correlated with DNA copy number. I hope to be able to submit this package to Bioconductor by the end of the summer. If you are interested in testing the package I will be happy to share it with you as soon as it will be stable enough to be distributed. In case you are attending ISMB/ECCB at the end of the month, I will be presenting a poster about this work: "GTCA: Genome Transcriptome Correlation Analysis within R" (poster number: I56) Cheers, Pierre. Sean Davis wrote: > Tarun Nayar wrote: >> Hi, >> >> Are there any tools out there to combine/ compare Affy gene expression >> and aCGH data? A collaborator has 12 aCGH expts and 12 affy expression >> chips from the same biological samples. He's interested in seeing if >> regions of CN alteration correspond to differences in gene expression. >> We've taken a stab at writing our own program for this, now I'm >> wondering if there are any pre-made tools to do the same. >> > > I don't know of R/bioc packages for doing this directly, but some > version of correlation between CGH measurements and gene expression > measures is probably useful. You can use standard R commands to do > this. Within any region of amplification, note that there will likely > be only a portion (of unknown quantity) of gene expression that is > correlated with copy number. > > Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > . >
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Hi Torun, Like Sean I too don't know of any currently available package to do so. However have a look at the following papers: 1. Stranger et. al.: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_u ids=17 289997 2. Spielman et. al.: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_u ids=17 206142 3. Chin et. al: http://linkinghub.elsevier.com/retrieve/pii/S1535610806003151 Benjamin ====================================== Benjamin Otto University Hospital Hamburg-Eppendorf Institute For Clinical Chemistry Martinistr. 52 D-20246 Hamburg Tel.: +49 40 42803 1908 Fax.: +49 40 42803 4971 ====================================== -----Urspr?ngliche Nachricht----- Von: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Sean Davis Gesendet: Saturday, July 07, 2007 9:25 PM An: Tarun Nayar Cc: bioconductor at stat.math.ethz.ch Betreff: Re: [BioC] Tools for Combining Affy and aCGH data Tarun Nayar wrote: > Hi, > > Are there any tools out there to combine/ compare Affy gene expression > and aCGH data? A collaborator has 12 aCGH expts and 12 affy expression > chips from the same biological samples. He's interested in seeing if > regions of CN alteration correspond to differences in gene expression. > We've taken a stab at writing our own program for this, now I'm > wondering if there are any pre-made tools to do the same. > I don't know of R/bioc packages for doing this directly, but some version of correlation between CGH measurements and gene expression measures is probably useful. You can use standard R commands to do this. Within any region of amplification, note that there will likely be only a portion (of unknown quantity) of gene expression that is correlated with copy number. Sean _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Pflichtangaben gem?? Gesetz ?ber elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universit?tsklinikum Hamburg-Eppendorf K?rperschaft des ?ffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. J?rg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus
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I have introduced an experimental approach to the combination of expression and CGH data in the Neve2006 package. This is available through the Browse packages/ExperimentData path on the portal. In the most recent devel version I introduce a class called cghExSet that has AssayData components for expression and logRatios, and accessors for both. a cloneMeta slot holds an annotated data frame that names and indexes clone locations both on chromosomes and along entire genome. I say it is experimental because I don't have proven workflow examples with it. But it seems to differ from the available CGH container designs in that it binds the sample level data directly to the CGH assay results (and it differs by keeping CGH and expression together). It is unusual to push a class design in an experimental data package but until I get comfortable with it I am keeping it close to the data; the class definitions can be migrated to Biobase (or some to-be-defined CGH infrastructure package) if appropriate. In fact I am not thrilled with the current design that I have but the interface seems ok -- that is, the [few] methods defined seem useful, and that is what we should focus on -- what are the methods that we want to interrogate this combination of data most thoroughly? And then the class definition can evolve to support those most efficiently. Last issue: the expression data is readily annotated because we know the platform (hgu133a) and its annotation; the clone data is not so easy because except for a table provided with the publication of the data to the web, i don't know the provenance of the location assertions. If there are manufactured clone sets used for CGH perhaps we need annotation packages for them, but I don't know how to pursue this. --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Mon, 9 Jul 2007, Benjamin Otto wrote: > Hi Torun, Like Sean I too don't know of any currently available package to do so. However have a look at the following papers: 1. Stranger et. al.: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_u ids=17 289997 2. Spielman et. al.: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_u ids=17 206142 3. Chin et. al: http://linkinghub.elsevier.com/retrieve/pii/S1535610806003151 Benjamin ====================================== Benjamin Otto University Hospital Hamburg-Eppendorf Institute For Clinical Chemistry Martinistr. 52 D-20246 Hamburg Tel.: +49 40 42803 1908 Fax.: +49 40 42803 4971 ====================================== -----Urspr??ngliche Nachricht----- Von: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Sean Davis Gesendet: Saturday, July 07, 2007 9:25 PM An: Tarun Nayar Cc: bioconductor at stat.math.ethz.ch Betreff: Re: [BioC] Tools for Combining Affy and aCGH data Tarun Nayar wrote: > Hi, > > Are there any tools out there to combine/ compare Affy gene expression > and aCGH data? A collaborator has 12 aCGH expts and 12 affy expression > chips from the same biological samples. He's interested in seeing if > regions of CN alteration correspond to differences in gene expression. > We've taken a stab at writing our own program for this, now I'm > wondering if there are any pre-made tools to do the same. > I don't know of R/bioc packages for doing this directly, but some version of correlation between CGH measurements and gene expression measures is probably useful. You can use standard R commands to do this. Within any region of amplification, note that there will likely be only a portion (of unknown quantity) of gene expression that is correlated with copy number. Sean _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Pflichtangaben gem???? Gesetz ??ber elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universit??tsklinikum Hamburg-Eppendorf K??rperschaft des ??ffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. J??rg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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