[BioC] edgeR: summary of differentially expressed genes or tags

[Gordon K Smyth]

Page 51 of the edgeR User's Guide (4 May 2012) gives an example of this.

Gordon

On Mon, 4 Jun 2012, KJ Lim wrote:

> Dear Prof Gordon,
>
> Thanks for your suggestion and explanation.
>
> How could I never thought about the expression (up or down-regulated) of
> same genes may change when test on multiple coefficients! Thanks for your
> time and help. Have a nice day.
>
> Best regards,
> KJ Lim
>
> On 4 June 2012 04:11, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>
>> Dear KJ Lim,
>>
>> When testing for multiple coefficients, the easiest way to learn the
>> number of differentially expressed genes is by:
>>
>>  FDR <- p.adjust(ltr$PValue, method="BH")
>>  sum(FDR < 0.05)
>>
>> There is however no unambiguous way to break this down by up and down
>> genes.  There is no unambiguous way to classify a gene as up or down with
>> respect to multiple coefficients, because the coefficients may change in
>> different directions for the same gene.
>>
>> Best wishes
>> Gordon
>>
>>  Date: Sat, 2 Jun 2012 18:19:32 +0300
>>> From: KJ Lim <jinkeanlim at gmail.com>
>>> To: Bioconductor mailing list <bioconductor at r-project.org>
>>> Subject: [BioC] edgeR: summary of differentially expressed genes or
>>>        tags
>>>
>>> Dear edgeR community,
>>>
>>> Good day.
>>>
>>> I can learn summary of the up and down regulated genes/tags from
>>> >summary(de <- decideTestsDGE(lrt))
>>> when the *coef *of *glmLRT*(the likelihood ratio test) is set to one
>>> degree
>>> of freedom.
>>>
>>> When the *coef* is set to i.e. 2:5; the decideTestsDGE doesn't work. It
>>> could be nice to see the summary of up and down regulated genes/tags when
>>> the *coef* is set i.e. 2:5.
>>>
>>> Thus, may I ask is there any method to learn the number of up and down
>>> regulated genes/tags when the *coef* of *glmLRT*(the likelihood ratio
>>> test) is
>>> set to all groups?
>>>
>>> Thank you very much for your guys time and help.
>>>
>>> Have a nice weekend.
>>>
>>> Best regards,
>>> KJ Lim
>>>
>>
>>
>> ______________________________**______________________________**__________
>> The information in this email is confidential and intended solely for the
>> addressee.
>> You must not disclose, forward, print or use it without the permission of
>> the sender.
>> ______________________________**______________________________**__________
>>
>

______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}