Question: limma applied to unbalanced micro-array experiment
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gravatar for ewre
3.0 years ago by
ewre220
United States
ewre220 wrote:

Hello,

I have a microarray gene expression dataset which consists of 5 treated samples and only 1 control samples. I know that this kind of unbalanced design is not good for differential gene expression analysis. what I want to know is that which kind of differential gene expression method is most proper for this dataset?
1. a simple t test with the hypothesis that the data has a normal distribution
2. non parametric tests like rank test or rankprod
3. more advanced methods like limma

thank you for your time.

ADD COMMENTlink modified 3.0 years ago by Devon Ryan92k • written 3.0 years ago by ewre220
0
gravatar for Devon Ryan
3.0 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

The most appropriate method is limma (regardless of whether you have a balanced design or not).

ADD COMMENTlink written 3.0 years ago by Devon Ryan92k

Hi Devon Ryan. thank you for your reply. Since I have only one sample as control, will limma handle this kind of situiation properly?

ADD REPLYlink written 3.0 years ago by ewre220

Yes it will.

ADD REPLYlink written 3.0 years ago by Devon Ryan92k
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