[BioC] Up & Downregulated genes using DESeq

[Wolfgang Huber]

Dear Ekta and Bruce

just for the record: Omar's initial question was how to export a result 
table from DESeq into text files for subsequent analysis e.g. by 
spreadsheets. That was answered by Steve.

Then a discussion started on fold change cutoffs that might be applied 
in addition to the criterion of statistical significance (p-value). 
People might enjoy various arbitrary choices here, including "2", but 
this has nothing to do with DESeq or with Omar's question.

	best wishes
	Wolfgang



Ekta Jain scripsit 03/27/2012 12:46 PM:
> I am not a statistician but from whatever experience i have had to find differentially expressed genes, the logFC cut off used has been of a two-fold change (increase or decrease). Of course, if in any analysis your fold change gene list needs be reduced or increased for number of genes you could change the two-fold threshold to zero or three.
>
> For a first off step, arbitrarily (as bruce also put it), two fold change seems ideal to use.
>
> Best,
> --E
>
>
>
> -----Original Message-----
> From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Bruce Moran(External)
> Sent: 27 March 2012 15:07
> To: Simon Anders; bioconductor at r-project.org
> Subject: Re: [BioC] Up&  Downregulated genes using DESeq
>
> Would be very interested to know how to define a fold change cutoff for
> RNAseq data. Doesn't seem to be any power analysis that might be of use.
>
> I use 2 (arbitrarily) also.
>
> Bruce.
>
> -----Original Message-----
> From: bioconductor-bounces at r-project.org
> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Simon Anders
> Sent: 27 March 2012 10:15
> To: bioconductor at r-project.org
> Subject: Re: [BioC] Up&  Downregulated genes using DESeq
>
> On 03/27/2012 06:34 AM, Ekta Jain wrote:
>> As far as i gather, the threshold for upregulated or downregulated
> genes should be>2FoldChange and>-2 FoldChange respectively. Not>0 or<0.
>
> Why 2?
>
>     Simon
>
> _______________________________________________
> 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
> ------------------------------------------------------------------------------
> Attention:
> This e-mail is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author.
> This email was scanned by Teagasc and has been certified virus free with the pattern file currently in use. This however cannot guarantee that it does not contain malicious content.
>
> Tabhair aire:
> Ta an r-phost seo faoi phribhleid agus faoi run. Mura tusa an duine a bhi beartaithe leis an teachtaireacht seo a fhail, scrios e le do thoil agus cuir an seoltoir ar an eolas. Is leis an udar amhain aon dearcai no tuairimi a leiritear.
> Scanadh an r-phost seo le Teagasc agus deimhniodh go raibh se saor o vioras leis an bpatrunchomhad ata in usaid faoi lathair. Ni feidir a rathu leis seo afach nach bhfuil abhar mailiseach ann.
>
> _______________________________________________
> 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
> The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, 
a!
>   nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email.
> www.jubl.com
>
> _______________________________________________
> 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


-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber