[BioC] question about limma

[Richard Friedman]

Katie,
------------------------------------------------------------



On Jun 16, 2010, at 4:36 PM, Richard Friedman wrote:

>
> On Jun 16, 2010, at 12:30 PM, Taylor, Katie wrote:
>
>> Hi,
>>
>> I just have a quick question. I have been using limma to create  
>> toptables looking at differences betwen 6 groups. When I look at  
>> the results of the toptables I assumed that positive logFC meant  
>> that the gene was upregulated and if negative then it was down  
>> regulated. Is this correct?

logFC in limma means expression experiment > expression control if the  
contrast matrix is set up to represent experimenr-control.
You can check this by hand in an excel spreadsheet of the output,  
normalized expression values.

I am sorry but I haven''t used MEV and can't answer about it.

I hope this helps,
Rich
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In Memoriam,
George Scithers

>> The reason that I ask is because I was doing some similar  
>> statistics using MEV software but the FC was the opposite way  
>> around. I have given an example below:
>>
>> group1 - group2
>>
>> in limma gene X = +, Y=+ and Z=-
>> in MEV gene X= - , Y= - and Z=+
>>
>> Similar genes are detected but now im unsure as to whether or not  
>> they are up regulated in the first or second group. Please can  
>> someone help me with this.
>>
>> Thank you in advance.
>>
>> Best wishes,
>>
>> Katie
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>