Question: Re: affylmGUI

0

James Wettenhall •

**1000**wrote:Pedro,
> I do not know if there is any forum where to ask people or
> share experience about this package.
The best place to discuss affylmGUI is on the Bioconductor
mailing list:
http://www.bioconductor.org/mailList.html
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
I hope you don't mind that I've copied my reply to the mailing
list, in case anyone out there wants to improve upon my answers.
> In the table with ranked genes differentially express what is
> the column M and A? are the values for the M A plot blot???
The terms M and A are most well known in the two-color
microarray literature, e.g. see:
http://www.statsci.org/smyth/pubs/mareview.pdf
but they can also be applied to Affymetrix arrays.
M is a log ratio comparing gene expression levels.
(Base 2 is used for the logarithm)
e.g. log_2(Mutant_expr_level/WildType_expr_level)
A is an average log intensity.
(Again, the logarithm is in base 2)
Obviously, you can't get absolute gene expression levels from
microarrays. For two-color arrays, the A value will depend on
the scanner intensity.
For two-color arrays it is actually a little confusing because
we use M to mean a log-ratio between the Red and Green channels
on one array, but later after we have averaged between replicate
arrays (or more formally, after we have fitted a linear model),
then we use M to mean a log-ratio between gene expression levels
(e.g. comparing Treatment vs Control or Wild-Type vs Mutant).
An M value of positive 1 means a fold-change of 2 and an M value
of -1 means a fold-change of 0.5 (or equivalently, a fold-change
of 2 in the other direction).
If you want to convert the M column to fold-changes you can use
=2^M in Excel, e.g. if the M column is column "E" and the first
M value was in cell E2, then you could create a column G
entitled "Fold Change", and in cell G2, you could type the
formula:
=2^E2
and then fill-down.
(I'm assuming that you know how to get the toptable into Excel
by first saving as tab-delimited text.)
FDR is False Discovery Rate, a method for multiple-testing
correction. I think the default method in
limma, limmaGUI, affylmGUI is:
Holm, S. (1979). A simple sequentially rejective multiple test
procedure. _Scandinavian Journal of Statistics_, *6*, 65-70.
For references to other multiple-testing correction methods,
from the R prompt, type:
?p.adjust
Hope this helps,
James
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James Wettenhall Tel: (+61 3) 9345
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Division of Genetics and Bioinformatics Fax: (+61 3) 9347
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