[BioC] upregulated or downregulated?

[biosciencegeek at gmail.com]

Thanks a million. Simple question but I couldn't get the answer. Very
kind of you, Saroj.
Regards
Eamonn

2009/5/25 Saroj K Mohapatra <saroj at vt.edu>:
>
>> i.e., calculating mean log intensities and then subtracting the reference
>> from the treated group value.
>>
> I meant subtracting the reference cancer from the other cancer 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
>>>
>>>    [[alternative HTML version deleted]]
>>>
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>



-- 
All the Best,

Eamonn