[BioC] 5 genes with 4 diff. groups, Howmany Cells needs to be extracted and do LIMMA?

[Naomi Altman]

You could use limma for this experiment but since you cannot use the eBayes 
procedure with so few genes you might be better off using a simpler 
statistical package such as SAS or MINITAB.

The routine you want is called one-way ANOVA.

Surely you do not intend to use microarrays with so few genes.  This cannot 
be cost-effective?

You need to have biological replication within group to do the analysis you 
suggest.

--Naomi

At 01:31 PM 6/23/2005, Saurin Jani wrote:
>Dear BioC,
>
>Please guide me in experient..Howmany Cells I need to
>collect in order to be confident in my LIMMA
>statistical analysis? I think LIMMA is the good
>approach because I hvae more than 2 conditions. Please
>see below information.
>
>I would like to perform experient of 5 genes with 4
>different groups of cells. ( Small scale array)
>
>
>          GeneA GeneB GeneC GeneD GeneE
>Group1
>Group2
>Group3
>Group4
>
>How can I define Design Matrix for these 4 different
>groups of cells?
>
>Can I do:
>
>Group1-Group2, Group1-Group3, Group1-Group4
>
>Group2-Group3, Group2-Group4
>
>Group3-Group4
>
>
>I would like to study on SMALL scale Array...Is there
>any approach which I could seek?
>
>Please, let me know if anybody has performed such
>design or analysis?
>
>Thank you so much in advance,
>Saurin
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111