How to output Normalised count data from DESeq?

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Fabrice Tourre ▴ 970

@fabrice-tourre-4394

Last seen 10.3 years ago

Dear list, I have got the raw counts for each exon using HTSeq-count. I want to use DESeq to normalise the counts. How can I output the Normalised count data from DESeq? Thank you

DESeq DESeq • 3.3k views

ADD COMMENT • link updated 13.3 years ago by Andreia Fonseca ▴ 810 • written 13.3 years ago by Fabrice Tourre ▴ 970

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Andreia Fonseca ▴ 810

@andreia-fonseca-3796

Last seen 7.9 years ago

Hi Fabrice, when you use DESeq after normalizing you get the size factors. I think that if you divide your count data by the size factor you get the normalized count. Kind regards, Andreia On Wed, Aug 17, 2011 at 12:29 AM, Fabrice Tourre <fabrice.ciup@gmail.com>wrote: > Dear list, > > I have got the raw counts for each exon using HTSeq-count. > I want to use DESeq to normalise the counts. How can I output the > Normalised count data from DESeq? > > Thank you > > _______________________________________________ > 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 > -- ---------------------------------------------------------------------- ----------------------- Andreia J. Amaral, PhD BioFIG - Center for Biodiversity, Functional and Integrative Genomics Instituto de Medicina Molecular University of Lisbon Tel: +352 217500000 (ext. office: 28253) email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt [[alternative HTML version deleted]]

ADD COMMENT • link 13.3 years ago Andreia Fonseca ▴ 810

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Hi Fabrice, you can use counts(x, normalized=TRUE) For more info, have a look at the manual page of the 'counts' accessor function. Best wishes Wolfgang Aug/17/11 9:25 AM, Andreia Fonseca scripsit:: > Hi Fabrice, > > when you use DESeq after normalizing you get the size factors. I think that > if you divide your count data by the size factor you get the normalized > count. > Kind regards, > Andreia > > On Wed, Aug 17, 2011 at 12:29 AM, Fabrice Tourre<fabrice.ciup at="" gmail.com="">wrote: > >> Dear list, >> >> I have got the raw counts for each exon using HTSeq-count. >> I want to use DESeq to normalise the counts. How can I output the >> Normalised count data from DESeq? >> >> Thank you >> >> _______________________________________________ >> 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 >> > > > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber

ADD REPLY • link 13.3 years ago Wolfgang Huber ★ 13k

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