Hi All:

Even after going through hand full of posts on log fold change, I could not
figure out how exactly it is calculated in LIMMA.

Please see following example.

 

Arrays 3 and 4 are dye swaps for arrays 1 and 2 (Arrays 1 and 2 are rep 1
and rep 2).

 

For Gene 1;

 

The M values are,

 


1

2

3

4


-1.1907

-1.00507

0.68244023

0.815401

 

And the A values are,

 


1

2

3

4


7.693117

6.218356

7.59435237

6.671801

 

After computing the linear model fit the output is,

 


logFC

AveExpr

t

P.Value

adj.P.Val

B


-0.9234

7.044406

-8.0598372

0.000229

0.00306

0.868682

 

I am wondering how the logFC (-0.9234) is gotten.

LIMMA user guide says M values are simply the log2 fold changes between
conditions.

 

Any help is appreciated.

Thanks

Jay


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