Dear all, Is there an easy way to read 300 Imagene files in XML format to Limma? Your help is highly appreciated. Sincerely, Wei Chen, PhD Assistant Professor Biostatistics Core, Karmanos Cancer Institute Department of Oncology, School of Medicine Wayne State University 87 E Canfield, 4th floor Detroit, MI 48201 Phone: (313) 576-8655 Fax: (313) 576-8656 E-mail: chenw@karmanos.org Better treatments. Better outcomes. ----------- Confidentiality Notice: This email message, including an...{{dropped:12}}

Dear all, Is there an easy way to read 300 Imagene files in XML format to Limma? Your help is highly appreciated. Sincerely, Wei Chen, PhD Assistant Professor Biostatistics Core, Karmanos Cancer Institute Department of Oncology, School of Medicine Wayne State University 87 E Canfield, 4th floor Detroit, MI 48201 Phone: (313) 576-8655 Fax: (313) 576-8656 E-mail: chenw@karmanos.org Better treatments. Better outcomes. ----------- Confidentiality Notice: This email message, including an...{{dropped:12}}

Hi, On Fri, Jan 11, 2013 at 9:36 AM, Chen, Wei <chenw at="" karmanos.org=""> wrote: > Hi Steve, > > I contact the developer of Limma. The package does not handle XML format. Yes, XML is an unusual way to store the data. But I am stuck with 300 files, not a small number. Is there an easy way to parse the XML to excel or txt? I have no idea of how easy it would be, as I've never seen what this data looks like. I suspect this task will, in some sense, be "easy" -- but it will also likely be extremely tedious. If you want to get fancy, my guess it that using XQuery is "the right" way to go, but if you have no experience w/ XQuery, it won't be so helpful. My guess is that you may have to end up writing (or getting someone else to write) some adhoc script that parses the XML files into tables using your favorite text processing language. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Dear Wei Chen, I have never read an XML file into R, but a google search tells me that "The XML package provides general facilities for reading and writing XML documents within R." If the XML files are converted into data frames, then the information can be input to limma. Best wishes Gordon > Date: Thu, 10 Jan 2013 15:10:31 +0000 > From: "Chen, Wei" <chenw at="" karmanos.org=""> > To: "'bioconductor at stat.math.ethz.ch'" > <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Limma and XML > > Dear all, > > Is there an easy way to read 300 Imagene files in XML format to Limma? > Your help is highly appreciated. > > Sincerely, > > Wei Chen, PhD > Assistant Professor > Biostatistics Core, Karmanos Cancer Institute > Department of Oncology, School of Medicine > Wayne State University > 87 E Canfield, 4th floor > Detroit, MI 48201 > Phone: (313) 576-8655 > Fax: (313) 576-8656 > E-mail: chenw at karmanos.org > Better treatments. Better outcomes. > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}