[BioC] limma report logFC confidence interval?

[Fraser Sim]

Hi Gordon,

I agree. This would be useful addition as some readers, especially
non-statisticians, would like to see the relative errors of the logFCs on
plots and tables.

Cheers,
Fraser

-----Original Message-----
From: bioconductor-bounces at r-project.org
[mailto:bioconductor-bounces at r-project.org] On Behalf Of Richard Friedman
Sent: Friday, January 28, 2011 11:21 AM
To: Bioconductor mailing list
Cc: Gordon Smyth
Subject: Re: [BioC] limma report logFC confidence interval?

Gordon,
	
I once has a paper returned for lack of CIs and I got out of it by
explaining that Limma didn't give them Still it would be helpful if they
were available as an option. Often the experimentalists I support want
"error bars" (whatever those bars mean) rather than p-values or fdrs.

Thanks and best wishes,
Rich
-----------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of
Biomedical Informatics (DBMI) Educational Coordinator, Center for
Computational Biology and Bioinformatics (C2B2)/ National Center for
Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer
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"Did he win the Nobel prize or the Ig Nobel prize for levitating the frog?".
Rose Friedman, age 14




On Jan 28, 2011, at 11:13 AM, Segal, Corrinne wrote:

> Hi,
>
> I too would find it useful to have the CI reported.
>
> Thanks,
>
> Corrinne
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch
> ] On Behalf Of Gordon K Smyth
> Sent: 30 October 2010 00:13
> To: Timothy Wu
> Cc: Bioconductor mailing list
> Subject: [BioC] limma report logFC confidence interval?
>
> Sunny's CI is exactly right.
>
> CIs could be an option in topTable(), but this the first request for 
> them, so the demand doesn't seem enough for now.
>
> Best wishes
> Gordon
>
>> Date: Fri, 29 Oct 2010 00:14:39 -0400
>> From: Sunny Srivastava <research.baba at gmail.com>
>> To: Timothy Wu <2huggie at gmail.com>
>> Cc: bioconductor <bioconductor at stat.math.ethz.ch>
>> Subject: Re: [BioC] limma report logFC confidence interval?
>>
>> Hello Thomas,
>> I am sure senior members of the list will have more to say, here is 
>> my $0.02.
>>
>> logFC is the coefficient of the treatment in your model. Assuming 
>> that you have a model with only one treatment
>>
>> log Int_g = b0 + b1 * trt
>>
>> b1 = logFC
>>
>> The CI of logFC can be found in the same manner as you would do in 
>> normal linear regression, but here instead of usual t(0.975, df) 
>> quantile, you should use the moderated t quantile ie t(0.975, 
>> df.residual +
>> df.prior)
>>
>> So the 95% CI for logFC will be
>>
>> logFC -+ t(0.975, fit3$df.residual + fit3$df.prior) * 
>> fit3$stdev.unscaled *
>> sqrt(fit3$s2.post)
>>
>>
>> Please correct me if I am wrong.
>>
>>
>> Thanks,
>> S.
>>
>> On Thu, Oct 28, 2010 at 7:46 AM, Timothy Wu <2huggie at gmail.com>
>> wrote:
>>
>>> HI,
>>>
>>> Is there a way to report the CI of logFC from topTable in limma? I 
>>> googled around and it doesn't seem easy to find. I was expecting the 
>>> option to be in topTable().
>>>
>>> Thanks,
>>>
>>> Timothy
>
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