[BioC] Re: limma plot error?

Gordon Smyth smyth at wehi.edu.au
Fri Dec 26 02:28:25 MET 2003

After some dialog we determined that the problem was that the genes were 
listed in a different order in the gal file than in the gpr files. Please 
note that readGAL() in limma assumes the genes to be listed in standard 
order, i.e., in the same order as in the gpr. This is not currently checked.


At 03:46 PM 24/12/2003, Simon Melov wrote:
>In the input data I have checked for correct assignation of block, column, 
>row (I am using gpr files) and gene identity. After normalization my 
>buffers (which are negative controls) are displayed across the range of A 
>values in the MA plot (as seen below). However, most of my buffers have 
>very low A values (if you calculate manually). Somehow, between loading 
>and calculation of the A values, limma is adjusting these buffer values so 
>that they are spread across the range. I have checked everything I can 
>(i.e. are the individual values (R, Rb etc) being pulled from the correct 
>columns in the gpr files, and being assigned to the correct position in 
>the matrix. They are.

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