[BioC] about limma linear models

[Gordon K Smyth]

Dear Gang Jiang,

It's hard to give you much help if you don't tell us what the sample names 
(BI,BM,BI2,BM2) stand for.  In particular you need to tell us what are 
biological replicates and what are technical.  If the same label appears 
twice in your targets frame, it is just a technical replicate of the 
first?

Best wishes
Gordon

> Date: Tue, 17 May 2011 09:39:58 +0800 (CST)
> From: ?? <sense_0109 at 126.com>
> To: "Naomi Altman" <naomi at stat.psu.edu>
> Cc: bioconductor <bioconductor at r-project.org>
> Subject: Re: [BioC] about limma linear models
>
> Thank you for your reply. actually I have two biological replicates in 
> my experiment, and I'm confident with the statistic power of limma with 
> your information.
>
>
> gang jiang
>
>
>
>
> At 2011-05-17 00:15:14£¬"Naomi Altman" <naomi at stat.psu.edu> wrote:
>
>> If you have biological replicates, then using LIMMA is preferred with
>> small sample sizes.  If you have only technical replicates, then you
>> really cannot do a proper statistical analysis of the data.  Since
>> you have a disconnected design, you might use separate channel
>> analysis to simplify the comparisons you want to make.
>>
>> Regards,
>> Naomi Altman
>>
>>
>> At 07:40 AM 5/16/2011, =?GBK?B?va241Q==?= wrote:
>>> Hello Everyone!
>>>
>>>
>>> I'm now working with my expression microarray data by limma to
>>> detect differential expression probes. I have biology as my
>>> knowledge background ,not statistics, so I'm confused with the
>>> design matrix and contrast matrix in the limma usersguide.  now i
>>> have read the target file
>>> as follows:
>>> SlideNumber   FileName Cy3 Cy5
>>> 1           1       15_1_3.txt  BI  BM
>>> 2           2       15_1_4.txt  BM  BI
>>> 3           3       18_1_2.txt BI2 BM2
>>> 4           4       18_1_3.txt BM2 BI2
>>> 5           5       16_1_1.txt BE2 BM2
>>> 6           6       16_1_2.txt BM2 BE2
>>>
>>>
>>> because there is no connection from BI(or BM) to the other samples,
>>> dose that mean I have to contrast the differences(BI-BM, BI2-BM2,
>>> BE2-BM2, BE2-BI2) separately?
>>> Though I read the linear models and Empirical Bayes Methods theory
>>> carefully, I only know little.  I wonder It is proper to detect
>>> differential expression by limma when there are only two replicates?