[BioC] upregulated or downregulated?

[Saroj K Mohapatra]

> 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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