[BioC] Interpretation Fold Change - Limma
pkpekka at gmail.com
Wed Nov 13 15:03:43 CET 2013
You can type the function write.fit(), which will write a file that
has all the statistics for the contrasts and fold changes. Fold
changes are in the Coef. columns. just type write.fit(fit,
Best Regards, Pekka
2013/11/12 Christian De Santis <christian.desantis at stir.ac.uk>:
> Hi All,
> a question about the interpretation of the logFC in limma. I have a microarray experiment with a common reference (Cy5) design.
> I have generated the two matrices in the following manner
> design.contrast <- modelMatrix(targets, ref="REF")
> contrast.matrix <- makeContrasts (BPCa0-BPCa20, BPCa0-BPCa40, BPCa0-BPCa60, levels=design.contrast)
> and fitted the linear model. No problems there.
> The contrast matrix looks like the following:
>> contrast.matrix [1:4,1:3]
> Levels BPCa0 - BPCa20 BPCa0 - BPCa40 BPCa0 - BPCa60
> BPCa0 1 1 1
> BPCa20 -1 0 0
> BPCa40 0 -1 0
> BPCa60 0 0 -1
> And the fitted coefficients for those contrasts:
> BPCa0 - BPCa20 BPCa0 - BPCa40 BPCa0 - BPCa60
> [1,] -0.07923765 -0.06255957 -0.14165962
> [2,] -0.18658108 0.10286377 -0.06617045
> [3,] -0.02428776 0.04029805 0.09705064
> For no reasons, i assumed that the output value would represent the log expression of the first group vs the second as in log(BPCa0/BPCa20) and therefore a negative value would mean downregulation in the first group compared with the second. I have evidence, however, to believe that this might not be the case (by checking the M values)...
> Could someone please clarify how do i correctly interpret this fold change as it is not straight forward for me to extract this information from the matrix.
> Thanks in advance,
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