[BioC] question about limma

[Mark Cowley]

Hi Katie,
i suggest that you check the levels of those genes across your samples in your original expression data. the true direction of the change will reveal itself.
cheers,
mark

On 17/06/2010, at 7:07 AM, michael watson (IAH-C) wrote:

> Hi Katie
> 
> Can you post the code you used in limma, and specifically, the design and contrast (if there was one) matrices
> 
> Mick
> ________________________________________
> 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
> 
> 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? 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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