[BioC] question about limma

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed Jun 16 23:07:22 CEST 2010

Hi Katie

Can you post the code you used in limma, and specifically, the design and contrast (if there was one) matrices

From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Taylor, Katie [kt70 at leicester.ac.uk]
Sent: 16 June 2010 17:30
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] question about limma


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? 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,

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