[BioC] upregulated or downregulated?
biosciencegeek at gmail.com
biosciencegeek at gmail.com
Mon May 25 03:43:26 CEST 2009
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
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