[BioC] Interpretation Fold Change - Limma

Pekka Kohonen pkpekka at gmail.com
Wed Nov 13 15:03:43 CET 2013


Dear Christian,

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,
file="xxx.txt")

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]
>         Contrasts
> 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:
>> fit.contrast$coefficients[1:3,1:3]
>       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,
> Christian
>
>
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