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@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@gmail.com>
>> To: Bioconductor mailing list <bioconductor@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
>>
>
>
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