[BioC] power calculation of RNA-Seq

[Yanzhu Lin]

Hi Professor Wu,

I have successfully loaded the vignette and have taken look at it, but I am
still not clear how to use the package for my project. The following is
some information about my project.

My project has a multi-factor design, which includes three factors: L with
16 levels, S with 2 levels and E with 3 levels, hence it ends up with  16 x
2 x 3 = 96 groups. There are 8 biological replicates within each group. We
already have our RNA-Seq read count data available.

I would like to test how much power we have for 8 biological replicate per
group based on the RNA-seq read count data we have.

BTW, in the vignette of PROPER, I didn't find the function works for
mulit-factor design, do you mind telling me where I can find the functions
work for multi-factor design? Thanks.



Best,


Yanzhu








On Wed, Sep 10, 2014 at 10:50 AM, Zhijin Wu <zwu at stat.brown.edu> wrote:

> Hi Yanzhu,
>   The vignette (software manual) is distributed with the PROPER package.
> Examples with code are given for various situations in the vignette. Just
> type
>
> vignette("PROPER")
>
> in R (after you load the package) and it should open up the pdf file.
>
> ------------------------------------
> Zhijin (Jean) Wu
> Associate Professor of Biostatistics
> Brown University, Box G-S121
> Providence, RI  02912
>
> Tel: 401 863 1230
> Fax: 401 863 9182
> http://www.stat.brown.edu/zwu
>
>
> On 9/10/2014 9:21 AM, Yanzhu Lin wrote:
>
>> Hi Dr. Wu,
>>
>> I am very interested in the package of power calculation of RNA-Seq data
>> with factorial design mentioned in your post and I would like to try it. I
>> have downloaded the package from the link you provided. But, I am not
>> clear
>> how to use it, could you give me an example about how to use it?
>>
>> Your help will be greatly appreciated.
>>
>>
>>
>> Best,
>>
>>
>> Yanzhu
>>
>>
>>
>>
>> On Tue, Jul 1, 2014 at 9:58 AM, Michael Love<michaelisaiahlove at gmail.com>
>> wrote:
>>
>> Let's keep the discussion on the list. This provides a searchable
>>> archive for other Bioc users with similar questions.
>>>
>>> A google search for "bioconductor rna-seq power calculation" reveals:
>>>
>>> http://www.bioconductor.org/packages/release/bioc/html/RNASeqPower.html
>>>
>>>
>>> On Tue, Jul 1, 2014 at 9:53 AM, Yanzhu Lin<mlinyzh at gmail.com>  wrote:
>>>
>>>>
>>>> Hi Michael,
>>>>
>>>> Do you happenly know there is any package or paper works for power
>>>>
>>> calculation of factorial design of RNA-Seq project? Thanks.
>>>
>>>>
>>>>
>>>> Best,
>>>>
>>>>
>>>> Yanzhu
>>>>
>>>
>>>
>>

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