Re: power calculation of RNA-Seq

Hi Hao,

Thank you very much for letting me know, I really appreciate it.


Best,


Yanzhu
On Thu, Sep 11, 2014 at 3:32 PM, Wu, Hao <[email protected]> wrote:

>  Yanzhu,
>
> Not sure whether Zhijin has answered. But unfortunately at this time,
> PROER only works for two-group comparison. Developing power calculation for
> general experimental design is on our todo list. Sorry we can't be more
> helpful for your data.
>
> Regards,
> Hao
>
>
>
>
>
> From: Yanzhu Lin <[email protected]>
> Date: Wednesday, September 10, 2014 2:40 PM
> To: Zhijin Wu <[email protected]>
> Cc: "[email protected]" <[email protected]>, "Wu, Hao" <
> [email protected]>
> Subject: Re: power calculation of RNA-Seq
>
>  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 <[email protected]> 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<[email protected]
>>> >
>>> 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<[email protected]>  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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