Hi Sunny,

Thanks so much. I am not using LIMMA for microarray data in this case. I
like LIMMA because of its capability of modeling and ebays function. It will
be a big plus if LIMMA can deal with other type of data. Thanks again and
much appreciated.

Speaking zero in this case, it is the true observations, not null value. I
am not sure how can I ignore them.

Steve

On Wed, Mar 30, 2011 at 2:01 PM, Sunny Srivastava
<research.baba@gmail.com>wrote:

> Hi Steve:
>
> I think LIMMA does the right thing by not having any link/family because it
> is meant *only* for log normal intensities. Using it for anything else is
> not correct.
>
> However, as you say you have a lot of 0s -- I would ignore them because you
> are trying to extract information where it is not available. You can do
> better by something like a zero-inflated modeling. But LIMMA is not meant
> for that purpose.
>
> I must say -- I am surprised you are modelling microarray data and you have
> zeros and observation between 0 and 1.
>
> Thanks,
> S.
>
>
>
> On Wed, Mar 30, 2011 at 11:55 AM, Steve Shen <sshen@bu.edu> wrote:
>
>> Hi Sunny,
>>
>> Thanks so much for your input. Then, how to deal with inf or missing value
>> after logit, because the data I am dealing with have lots of zeros in many
>> samples. Any opinion? I wish that LIMMA can provide some link/family type of
>> arguments just like GLM does. Thanks a lot.
>>
>> Steve
>>
>>
>> On Wed, Mar 30, 2011 at 6:46 AM, Sunny Srivastava <
>> research.baba@gmail.com> wrote:
>>
>>> Hi Steve:
>>>
>>> I am sure Prof. Smyth and others will have better insights but here is my
>>> $0.02.
>>>
>>> I would transform the data using the logit transform, that is,
>>>
>>> x_ij goes to log (x_ij / ( 1 - x_ij) )  ## with boundary value correction
>>> when x_ij = 0 or 1
>>>
>>> And then use LIMMA.
>>>
>>> This makes sure that the data you are working with lies in [-Inf, Inf]
>>> interval.
>>>
>>> Thx,
>>> S.
>>>
>>> On Tue, Mar 29, 2011 at 8:44 PM, Steve Shen <sshen@bu.edu> wrote:
>>>
>>>> Hello list,
>>>>
>>>> Can LIMMA work with beta distributed interval(0,1) data? Thanks,
>>>>
>>>> Steve
>>>>
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>>>
>>>
>>
>

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