Bioconductor Digest, Vol 86, Issue 19
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@sherri-christian-4030
Last seen 10.5 years ago
Hi Christoph, First, install the package as suggested by Benilton - the name that you tried was not correct >biocLite("hugene10stv1.r3cdf") Then load the library >library("hugene10stv1.r3cdf") Then read in your data >data <- ReadAffy() #will read in all CEL files in your working directory Then tell Affy which cdf file it needs to use- because the name of the CDF file that Affy thinks it needs is NOT what you downloaded >data at cdfName <- "hugene10stv1.r3cdf" Now check your data to be sure that the correct cdf file was used >data good luck, Sherri Date: Mon, 19 Apr 2010 01:51:17 +0100 From: Benilton Carvalho <beniltoncarvalho@gmail.com> To: Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Bioconductor - hugene10stv1cdf not available Message-ID: <v2se71a39ea1004181751p8be0629cnb483027cda4c1b95 at="" mail.gmail.com=""> Content-Type: text/plain; charset=windows-1252 btw, if you want to use the affy package, I believe that the package: http://www.bioconductor.org/packages/release/data/annotation/html/ hugene10stv1.r3cdf.html should suffice (you will need to specify the name of the package to be used though, check the docs for ReadAffy). b On Mon, Apr 19, 2010 at 1:48 AM, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > Hi Christoph, > > the way to do this with oligo is: > > library(oligo) > rawData = read.celfiles(list.celfiles()) > summaries1 = rma(rawData, target="probeset") > summaries2 = rma(rawData, target="core") > > summaries1 will contain the rma summaries to the probeset defined in > the PGF file. summaries2 will contain the summaries for the > metaprobesets defined in the core.mps file. > > AffyBatch objects are to be used with the affy package, so that's why > the pd.hugene package was of no use (b/c pd.hugene is to be used with > oligo). > > hth, > b > > On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp > <mkna005 at="" aucklanduni.ac.nz=""> wrote: > >> I forgot to mention that I tried that as well: >> >> >>> ? ? biocLite("hugene10stv1cdf") >>> >> Using R version 2.10.1, biocinstall version 2.5.10. >> Installing Bioconductor version 2.5 packages: >> [1] "hugene10stv1cdf" >> Please wait... >> >> Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> ?package ?hugene10stv1cdf? is not available >> >> Why is it not possible for me to install that package. >> >> Thanks >> >> Christoph >> >> On 19 April 2010 12:13, Christoph Knapp >> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >> >>> Sorry, >>> still no change >>> >>> AffyBatch object >>> size of arrays=1050x1050 features (11 kb) >>> cdf=HuGene-1_0-st-v1 (??? affyids) >>> number of samples=7 >>> Error in getCdfInfo(object) : >>> ?Could not obtain CDF environment, problems encountered: >>> Specified environment does not contain HuGene-1_0-st-v1 >>> Library - package hugene10stv1cdf not installed >>> Bioconductor - hugene10stv1cdf not available >>> In addition: Warning message: >>> missing cdf environment! in show(AffyBatch) >>> >>> Christoph >>> >>> On 19 April 2010 11:51, Benilton Carvalho >>> <beniltoncarvalho at="" gmail.com=""> wrote: >>> >>>> the pd.hugene package (which I'd expect you to download from >>>> BioC) is >>>> to be used with the oligo package. >>>> >>>> b >>>> >>>> On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp >>>> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>>> >>>>> Hi all, >>>>> I'm trying for quite some time to get an analysis started. I keep >>>>> getting this Error. >>>>> >>>>> Error in getCdfInfo(object) : >>>>> ?Could not obtain CDF environment, problems encountered: >>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>> Library - package hugene10stv1cdf not installed >>>>> Bioconductor - hugene10stv1cdf not available >>>>> Calls: rma ... .local -> indexProbes -> indexProbes -> .local - >>>>> > getCdfInfo >>>>> Execution halted >>>>> >>>>> I installed all possible packages from there >>>>> >>>>> http://www.bioconductor.org/docs/workflows/oligoarrays/ >>>>> >>>>> and even downloaded and installed that one >>>>> >>>>> http://mbi00206.bio.med.uni-muenchen.de/free/pd.hugene. >>>>> 1.0.st.v1.zip) >>>>> >>>>> still no change. >>>>> >>>>> What am I missing? >>>>> >>>>> It reads in the CEL files >>>>> >>>>> VFdata=ReadAffy() >>>>> >>>>> but when I look at the VFdata object it already says >>>>> >>>>> >>>>>> VFdata >>>>>> >>>>> AffyBatch object >>>>> size of arrays=1050x1050 features (11 kb) >>>>> cdf=HuGene-1_0-st-v1 (??? affyids) >>>>> number of samples=7 >>>>> Error in getCdfInfo(object) : >>>>> ?Could not obtain CDF environment, problems encountered: >>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>> Library - package hugene10stv1cdf not installed >>>>> Bioconductor - hugene10stv1cdf not available >>>>> In addition: Warning message: >>>>> missing cdf environment! in show(AffyBatch) >>>>> >>>>> and going on >>>>> >>>>> >>>>>> eset = exprs(rma(VFdata)) >>>>>> >>>>> Error in getCdfInfo(object) : >>>>> ?Could not obtain CDF environment, problems encountered: >>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>> Library - package hugene10stv1cdf not installed >>>>> Bioconductor - hugene10stv1cdf not available >>>>> Error in exprs(rma(VFdata)) : >>>>> ?error in evaluating the argument 'object' in selecting a >>>>> method for >>>>> function 'exprs' >>>>> >>>>>> >>>>>> >>>>> >>>>> I'm very inexperienced in terms of stuff like that. A answer for >>>>> dummies would be much appreciated. >>>>> >>>>> Thanks >>>>> >>>>> Christoph
cdf affy oligo cdf affy oligo • 1.1k views
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