[lumi] methyLumiR upload error of 450k

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Geoff Woodward ▴ 30

@geoff-woodward-5057

Last seen 10.2 years ago

Dear All, I've just started working with 450k data. I'm trying out a few different Bioconductor packages but keep running into problems. When I read the "FinalReport" from GenomeStudio with lumiMethyR() I get the following error: > testData <- lumiMethyR(filename="FinalReport.txt", lib="IlluminaHumanMethylation450k.db") Error in .getFinalReportBlock(filename, blockname = blockname, blocks = blocks, : The block called "[SAMPLE METHYLATION PROFILE]" in the file "E:/5975819001/ExtractionMethodFinalReport.txt" is not present and needs to be. Please re-export from beadstudio > But when I create the report, I check all of the options to make sure I'm not missing anything (even though this obviously makes the files huge). Any ideas? I've managed to load IDAT files through the lumimethy package, is there a way of converting the resulting MethylumiSet to MethyLumi? Any help would be amazing, Thanks! Geoff ----------------------------------------- Geoff Woodward Research Associate in Bioinformatics School of Social and Community Medicine University of Bristol Oakfield House Oakfield Grove Clifton Bristol BS8 2BN E: geoff.woodward at bristol.ac.uk T: 0117 33 13315

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ADD COMMENT • link updated 12.9 years ago by wei wang ▴ 20 • written 12.9 years ago by Geoff Woodward ▴ 30

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wei wang ▴ 20

@wei-wang-5058

Last seen 10.2 years ago

Dear Geoff, When you open your "**FinalReport.txt" file using any text editor, do you see [Header] in the first line, and [Sample Methylation Profile] in about the 8th line? Also check if there are extra blanks at the end of the first several lines. Sometimes the extra blanks will mess up the reading. To convert MethyLumiSet to MethyLumi, you can try this: new_MethyLumi_data <- as(old_MethyLumiSet_data, "MethyLumi") Wei [[alternative HTML version deleted]]

ADD COMMENT • link 12.9 years ago wei wang ▴ 20

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lumIDAT() will put the IDAT files into a MethyLumiM object as(mlumi, 'MethyLumiM') will coerce an existing MethyLumiSet into a MethyLumiM object hope this helps, --t On Wed, Jan 18, 2012 at 11:43 AM, wei wang <biowendy@gmail.com> wrote: > Dear Geoff, > > When you open your "**FinalReport.txt" file using any text editor, do you > see [Header] in the first line, and [Sample Methylation Profile] in about > the 8th line? Also check if there are extra blanks at the end of the first > several lines. Sometimes the extra blanks will mess up the reading. > > To convert MethyLumiSet to MethyLumi, you can try this: > new_MethyLumi_data <- as(old_MethyLumiSet_data, "MethyLumi") > > Wei > > [[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 > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]

ADD REPLY • link 12.9 years ago Tim Triche ★ 4.2k

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Thanks that's perfect! --On 18 January 2012 14:25 -0800 "Tim Triche, Jr." <tim.triche at="" gmail.com=""> wrote: > lumIDAT() will put the IDAT files into a MethyLumiM object > > > as(mlumi, 'MethyLumiM') will coerce an existing MethyLumiSet into a > MethyLumiM object > > > hope this helps, > > > --t > > > > > > On Wed, Jan 18, 2012 at 11:43 AM, wei wang <biowendy at="" gmail.com=""> wrote: > > Dear Geoff, > > When you open your "**FinalReport.txt" file using any text editor, do you > see [Header] in the first line, and [Sample Methylation Profile] in about > the 8th line? ?Also check if there are extra blanks at the end of the > first > several lines. ?Sometimes the extra blanks will mess up the reading. > > To convert MethyLumiSet to MethyLumi, you can try this: > new_MethyLumi_data <- as(old_MethyLumiSet_data, "MethyLumi") > > Wei > > ? ? ? ?[[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > If people do not believe that mathematics is simple, > it is only because they do not realize how complicated life is. > > John von Neumann ----------------------------------------- Geoff Woodward Research Associate in Bioinformatics School of Social and Community Medicine University of Bristol Oakfield House Oakfield Grove Clifton Bristol BS8 2BN E: geoff.woodward at bristol.ac.uk T: 0117 33 13315

ADD REPLY • link 12.9 years ago Geoff Woodward ▴ 30

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