[BioC] upregulated or downregulated?

[Saroj K Mohapatra]

Hi,

In the log-scale , positive value suggests up-regulation; negative 
down-regulation. For example: 2-fold up-regulation gives logFC of 1, 
2-fold down-regulation (i.e., 0.5) gives -1.

 > log2(2)
[1] 1
 > log2(0.5)
[1] -1

In the example you provided, genes 1-11 are up-regulated; the rest down.

This assumes that the design and contrast matrices have been set up 
correctly. You might want to check manually the logFC result against the 
actual result for a few genes, i.e., calculating mean log intensities 
and then subtracting the reference from the treated group value.

Best,

Saroj

biosciencegeek at gmail.com wrote:
> Hi,
> I have searched the mailing list but have found no solution.I have a set of
> 19 genes from two cancer types from a single dye experiment that have been
> analysed by limma. How do I know by looking at the logFC values which genes
> have been upregulated and downregulated?
>
> *Gene logFC              adjusted p value*
> 1      4.503176282     8.16484E-07
> 2      3.098042379     0.001186095
> 3      2.478184614     6.25887E-06
> 4      2.123900966     0.000345836
> 5      2.072218463     0.000307254
> 6      1.861216801     0.019495491
> 7      1.60330851       0.000170216
> 8      1.371819046     0.041850715
> 9      1.32421397       0.002931049
> 10     1.290754778    1.6091E-05
> 11     1.110357905    0.011299876
> 12     -0.638346118   0.046342014
> 13     -0.661346419   0.019450208
> 14     -0.67761362     0.046342014
> 15     -0.90175871     0.020400911
> 16     -0.904514183   0.014558953
> 17     -1.015572133   0.046342014
> 18     -1.545921472   5.24644E-05
> 19     -3.499508887   1.58919E-06
>
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