Bioconductor Digest, Vol 128, Issue 7
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@manvendra-singh-6279
Last seen 8.1 years ago
Dear All, I am using virtualArray package, I have the same error which Michael had few days back, but I could not get solution of that question. I am Analyzing various cross-species micro-array data from different platforms exactly as paper suggests. when I run final script as > virtualArrayExpressionSets() I get following error > bplasterror() 2/6 partial results stored. First 4 error messages: [2]: Error: Error in eval(expr, envir, enclos): object 'hgu133plus2SYMBOL' not found [3]: Error: Error in eval(expr, envir, enclos): object 'GPL6244SYMBOL' not found [5]: Error: Error in eval(expr, envir, enclos): object 'GPL6885SYMBOL' not found [6]: Error: Error in eval(expr, envir, enclos): object 'GPL6244SYMBOL' not found I am early stage PhD student and little frustrated about it as I require it urgently because of my supervisor. I ccd this message to Michael as well, Please reply me that how to solve this issue, I would be grateful. best reagrds Sincerely Yours Manvendra Singh [[alternative HTML version deleted]]
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@manvendra-singh-6279
Last seen 8.1 years ago
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@federico-lasa-6147
Last seen 8.1 years ago
Hi, No, the "2" is intentional. It is a table that 'maps' affy probe ids TO (sounds like two) gene symbols. I'm just guessing here, but i think that you need to install and load the hgu133plus2.db package. try running: source("http://bioconductor.org/biocLite.R") biocLite("hgu133plus2.db") library("hgu133plus2.db") If you do that, you'll see by calling it that hgu133plus2SYMBOL is now loaded. However, as I said, I'm merely guessing. If you share more info on the output you get when calling your expression sets it'll be helpful, also don't forget to reply to all so other people on the list can see this, I forgot to do that on my first reply. cheers. On Sat, Dec 7, 2013 at 6:44 AM, Manvendra Singh <mnujnu@gmail.com> wrote: > Dear Federico, > Many Thanks for your prompt reply. > I am comparing cross-platform, cross-species gene expression. virtualArray > seems to be good tool for the same., I have to filter out orthologous genes > for which common probes are there in each platform and then to plot a > correlation matrix between samples after batch effect correction. > > If error is "" Error: Error in eval(expr, envir, enclos): object > 'hgu133plus2SYMBOL' not found""" > then I think there is error in code because isn't it missing $ before > symbol?????/ > > I cordially appreciate your reply. > > Thanks again > Manu > > > > > On Fri, Dec 6, 2013 at 7:45 PM, Federico Lasa <felasa@gmail.com> wrote: > >> Hi, >> >> Looks to me like you need to load some annotation packages, try >> installion the following packages: >> >> -hgu133plus2.db and posssibly hgu133plus2probe >> >> -GPL6224 corresponds to Gene ST 1.0 v1 by affy so the corresponding >> annotation package is hugene10sttranscriptcluster.db. >> >> - GPL6885 corresponds to Illumina MouseRef-8 v2.0. so the corresponding >> package is illuminaMousev2.db >> >> >> or you may just need to change the annotattion slot for the data sets to >> make them match the corresponding annotation packages in bioconducto. But >> i'm not familiar with what you're trying to do, but that's what i would >> try. Good luck. >> >> >> On Fri, Dec 6, 2013 at 10:48 AM, Manvendra Singh <mnujnu@gmail.com>wrote: >> >>> Dear All, >>> I am using virtualArray package, >>> I have the same error which Michael had few days back, but I could not >>> get >>> solution of that question. >>> I am Analyzing various cross-species micro-array data from different >>> platforms >>> exactly as paper suggests. when I run final script as >>> >>> > virtualArrayExpressionSets() >>> >>> I get following error >>> >>> > bplasterror() >>> >>> 2/6 partial results stored. First 4 error messages: >>> [2]: Error: Error in eval(expr, envir, enclos): object >>> 'hgu133plus2SYMBOL' >>> not found >>> >>> >>> [3]: Error: Error in eval(expr, envir, enclos): object 'GPL6244SYMBOL' >>> not >>> found >>> >>> >>> [5]: Error: Error in eval(expr, envir, enclos): object 'GPL6885SYMBOL' >>> not >>> found >>> >>> >>> [6]: Error: Error in eval(expr, envir, enclos): object 'GPL6244SYMBOL' >>> not >>> found >>> >>> I am early stage PhD student and little frustrated about it as I require >>> it >>> urgently because of my supervisor. >>> I ccd this message to Michael as well, Please reply me that how to solve >>> this issue, I would be grateful. >>> >>> best reagrds >>> Sincerely Yours >>> Manvendra Singh >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > > [[alternative HTML version deleted]]
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