Searching for packages for normalizing Metabolomic data
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@nqueraltclinicubes-4369
Last seen 6.8 years ago
Hi everybody, I am a beginner in the steps of preprocessing and data analysis of non-targeted metabolomic profiling experiments. Anyone knows if there exists some tool for normalizing this type of data (raw data or XCMS matrix data) in bioconductor? Many thanks in advance. Best regards, Núria ------------------------------------------------------- Núria Queralt Rosinach, Ph.D Bioinformatics technician Bioinformatics Unit IDIBAPS Edifici CEK C/ Rosselló, 153 08036 Barcelona TE: +34 93 227 5400 (ext 4523) Email: nqueralt@clinic.ub.es Web: http://bioinformatics.fcrb.es/bioinformatics/ [[alternative HTML version deleted]]
Preprocessing Preprocessing • 891 views
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@laurent-gatto-5645
Last seen 23 hours ago
Belgium
Dear N?ria, On 1 December 2010 12:20, <nqueralt at="" clinic.ub.es=""> wrote: > Hi everybody, > > > > I am a beginner in the steps of preprocessing and data analysis of non-targeted metabolomic profiling experiments. Anyone knows if there exists some tool for normalizing this type of data (raw data or XCMS matrix data) in bioconductor? Many thanks in advance. > In addition to Martin's hints, note that xcms also has it's own mailing list: http://masspec.scripps.edu/xcms/mailinglist.php Best wishes, Laurent > > Best regards, > > > > N?ria > > > > > > ------------------------------------------------------- > N?ria Queralt Rosinach, Ph.D > > Bioinformatics technician > Bioinformatics Unit > IDIBAPS > Edifici CEK > C/ Rossell?, 153 > 08036 Barcelona > TE: +34 93 227 5400 (ext 4523) > > Email: nqueralt at clinic.ub.es > Web: http://bioinformatics.fcrb.es/bioinformatics/ > > > > > ? ? ? ?[[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 >
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On 12/01/2010 09:35 AM, Laurent Gatto wrote: > Dear N?ria, > > On 1 December 2010 12:20, <nqueralt at="" clinic.ub.es=""> wrote: >> Hi everybody, >> >> >> >> I am a beginner in the steps of preprocessing and data analysis of non-targeted metabolomic profiling experiments. Anyone knows if there exists some tool for normalizing this type of data (raw data or XCMS matrix data) in bioconductor? Many thanks in advance. >> > > In addition to Martin's hints, note that xcms also has it's own > mailing list: http://masspec.scripps.edu/xcms/mailinglist.php and a brand new sig http://bioconductor.org/help/mailing-list/ https://stat.ethz.ch/mailman/listinfo/bioc-sig-proteomics arising out of enthusiasm at the recent Developer conference in Heidelberg. Martin > > Best wishes, > > Laurent > >> >> Best regards, >> >> >> >> N?ria >> >> >> >> >> >> ------------------------------------------------------- >> N?ria Queralt Rosinach, Ph.D >> >> Bioinformatics technician >> Bioinformatics Unit >> IDIBAPS >> Edifici CEK >> C/ Rossell?, 153 >> 08036 Barcelona >> TE: +34 93 227 5400 (ext 4523) >> >> Email: nqueralt at clinic.ub.es >> Web: http://bioinformatics.fcrb.es/bioinformatics/ >> >> >> >> >> [[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 >> > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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hemi.luan ▴ 10
@hemiluan-11345
Last seen 2.6 years ago

 

You can use the "statTarget" package for normalization of your data by using QC-RLSC. It can directly convert the xcmd file into input files.  http://www.bioconductor.org/packages/devel/bioc/vignettes/statTarget/inst/doc/statTarget.html

 

Sincerely,

Hemi

Hong Kong Baptist University

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