snapCGH
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João Fadista ▴ 500
@joao-fadista-1942
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@sean-davis-490
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On Monday 20 November 2006 10:55, Jo??o Fadista wrote: > Hi everyone, > > As I read the "snapCGH: Segmentation, Normalization and Processing of aCGH > Data User?s Guide" I became really excited with all the features in it to > analyse CGH data and because it is designed to be used in conjunction with > limma package, which I have already been using. I have done the practicals > and browsed the main functions using the data given in the package. > > After this stage I wanted to deal with a real data set so I downloaded a > CGH experiment from GEO (Gene Expression Omnibus) and put it on R workspace > using the GEOquery package. After that I converted the GEO DataSet into an > MAList to be able to use the data with snapCGH package. > > Despite of this, when I used the function processCGH it gave me an error: > > MA2 <- processCGH(MA, method.of.averaging=mean, ID="ID") > > Error in processCGH(MA, method.of.averaging = mean, ID = "ID") : $design > component is null > > So, then I managed to to make the design column, but it gave me an error, but a different one: > > MA$design <- rep(1,10) > > > > MA2 <- processCGH(MA, method.of.averaging=mean, ID="ID") > > Error in order(na.last, decreasing, ...) : argument 1 is not a vector > > > > Therefore, if MA is an object of class MAList this function should work. I > do not see what is wrong. Isn?t the snapCGH package compatible with the > GEO datasets? > > There is also another thing. In the examples folder of the package, the > clones.info file has the columns Chromosome and Position, but in the > dataset from GEO there is only the Entrez.GeneID identifier. Do you know of > anyway I could convert one into another? Hi, Joao. All the CGH methods that are available via bioconductor require a chromosome and basepair position. They cannot work without these. There are a number of ways to get chromosome location, but perhaps the simplest is to use the biomaRt package to go from gene_id to chromosome and position. I don't think that you will be able to proceed without having the chromosome locations included in the MA$genes data frame and, although I am not sure, I would guess that the error is because of not having these. Perhaps others on the list will confirm this. Sean
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Hi As Sean has said the methods available within snapCGH won't work if the Position and Chromosome elements aren't present in the $genes dataframe. However I think the error you are currently seeing isn't related to that. The processCGH function averages replicates of the clones and the ID argument specifies which column in $genes contains an identifier for each clone. If you don't have such an identifier then the easiest thing to do is add a column with the name "ID" to $genes with the numbers from 1 to the length of the genes dataframe. Hopefully the processCGH function will then work Mike Smith Quoting Sean Davis <sdavis2 at="" mail.nih.gov="">: > On Monday 20 November 2006 10:55, Jo?o Fadista wrote: >> Hi everyone, >> >> As I read the "snapCGH: Segmentation, Normalization and Processing of aCGH >> Data User?s Guide" I became really excited with all the features in it to >> analyse CGH data and because it is designed to be used in conjunction with >> limma package, which I have already been using. I have done the practicals >> and browsed the main functions using the data given in the package. >> >> After this stage I wanted to deal with a real data set so I downloaded a >> CGH experiment from GEO (Gene Expression Omnibus) and put it on R workspace >> using the GEOquery package. After that I converted the GEO DataSet into an >> MAList to be able to use the data with snapCGH package. >> >> Despite of this, when I used the function processCGH it gave me an error: >> > MA2 <- processCGH(MA, method.of.averaging=mean, ID="ID") >> >> Error in processCGH(MA, method.of.averaging = mean, ID = "ID") : $design >> component is null >> >> So, then I managed to to make the design column, but it gave me an error, > but a different one: >> > MA$design <- rep(1,10) >> > >> > MA2 <- processCGH(MA, method.of.averaging=mean, ID="ID") >> >> Error in order(na.last, decreasing, ...) : argument 1 is not a vector >> >> >> >> Therefore, if MA is an object of class MAList this function should work. I >> do not see what is wrong. Isn?t the snapCGH package compatible with the >> GEO datasets? >> >> There is also another thing. In the examples folder of the package, the >> clones.info file has the columns Chromosome and Position, but in the >> dataset from GEO there is only the Entrez.GeneID identifier. Do you know of >> anyway I could convert one into another? > > Hi, Joao. > > All the CGH methods that are available via bioconductor require a chromosome > and basepair position. They cannot work without these. There are a number > of ways to get chromosome location, but perhaps the simplest is to use the > biomaRt package to go from gene_id to chromosome and position. I don't think > that you will be able to proceed without having the chromosome locations > included in the MA$genes data frame and, although I am not sure, I would > guess that the error is because of not having these. Perhaps others on the > list will confirm this. > > Sean > >
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Hi everybody, I am trying to annotate my dataset (home spotted array, two colors, mice) using AnnBuilder. Every time I run the program the connection with the kegg website is not working, so I am able to build the annotation package but not for the kegg pathways. Does anybody know how to fix this problem or did anybody find a way to by pass it (like downloading a list of accession numbers and corresponding pathways)? here my script: ********************************************************************** ******************************* library(AnnBuilder) #Loading required package: Biobase #Loading required package: tools #Welcome to Bioconductor # Vignettes contain introductory material. To view, # simply type: openVignette() # For details on reading vignettes, see # the openVignette help page. #Loading required package: annotate library(GO) sessionInfo() #Version 2.3.1 (2006-06-01) #i386-pc-linux-gnu # #attached base packages: #[1] "splines" "tools" "methods" "stats" "graphics" #"grDevices" #[7] "utils" "datasets" "base" # #other attached packages: # # globaltest vsn limma multtest # "4.2.0" "1.10.0" "2.7.3" "1.10.2" # survival affydata affy affyio # "2.20" "1.8.0" "1.10.0" "1.0.0" # KEGG GO AnnBuilder RSQLite # "1.12.0" "1.12.0" "1.10.0" "0.4-1" # DBI annotate XML Biobase # "0.1-10" "1.10.0" "0.99-7" "1.10.0" mySrcUrls <- getSrcUrl("all", organism="Mus Musclusus") base<- file.path(.path.package("AnnBuilder"), "data", "lgtc.ids.1.txt") myBaseType<- "gbNRef" ABPkgBuilder(baseName=base, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = "lgtc201106", pkgPath = ".", organism ="Mus Musclusus", version ="1.1.0", author = list(author = "Paola Pedotti", maintener ="Paola Pedotti <p.pedotti at="" lumc.nl="">") ) #Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways//07214.gene #Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways//07215.gene #Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways//07216.gene #Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways//07217.gene #Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways//07218.gene #[1] "0 2 2" #Warning message: #cannot open file '/usr/local/lib/R/site-library/AnnBuilder/templates/PKGNAMEGO.1.Rd', reason 'No such file or directory' #The following data sets have been added to the database and will be removed: # [1] "./lgtc161106/data/lgtc161106ACCNUM.rda" # [2] "./lgtc161106/data/lgtc161106CHR.rda" # [3] "./lgtc161106/data/lgtc161106ENZYME.rda" # [4] "./lgtc161106/data/lgtc161106GENENAME.rda" # [5] "./lgtc161106/data/lgtc161106GO.1.rda" # [6] "./lgtc161106/data/lgtc161106GO2ALLPROBES.rda" # [7] "./lgtc161106/data/lgtc161106GO2PROBE.rda" # [8] "./lgtc161106/data/lgtc161106GO.rda" # [9] "./lgtc161106/data/lgtc161106LOCUSID.rda" #[10] "./lgtc161106/data/lgtc161106MAPCOUNTS.rda" #[11] "./lgtc161106/data/lgtc161106MAP.rda" #[12] "./lgtc161106/data/lgtc161106OMIM.rda" #[13] "./lgtc161106/data/lgtc161106ORGANISM.rda" #[14] "./lgtc161106/data/lgtc161106PATH.rda" #[15] "./lgtc161106/data/lgtc161106PMID2PROBE.rda" #[16] "./lgtc161106/data/lgtc161106PMID.rda" #[17] "./lgtc161106/data/lgtc161106QCDATA.rda" #[18] "./lgtc161106/data/lgtc161106QC.rda" #[19] "./lgtc161106/data/lgtc161106REFSEQ.rda" #[20] "./lgtc161106/data/lgtc161106SUMFUNC.rda" #[21] "./lgtc161106/data/lgtc161106SYMBOL.rda" #[22] "./lgtc161106/data/lgtc161106UNIGENE.rda" #Warning message: #Can't copy /usr/local/lib/R/site-library/AnnBuilder/templates/PKGNAMEGO.1.Rd in: copyTemplates(repList, pattern, pkgName, pkgPath) ********************************************************************** ******************************* thank you in advance Paola _______________________________________ Center for Human and Clinical Genetics Leiden University Medical Center Postzone: S-04-P, Postbus 9600 2300 RC Leiden, The Netherlands Telephone: +31 71 526 9440 Fax: +31 71 526 8285
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João Fadista ▴ 500
@joao-fadista-1942
Last seen 9.6 years ago
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