[BioC] lmFit: how method I use in non-Affy single channel
Marcelo Luiz de Laia
mlaia at fcav.unesp.br
Thu Apr 7 20:20:02 CEST 2005
Dear limma users,
The function lmFit have 3 methods. One, default, use gls.series and
another, robust, use rlm.series from MASS package. In help, gls.series
is mentioned to be used in hight correlation between spots replication.
In my case I dont have this.
I visited the help files but I dont get knowledge for decide how I use
in my data set. The method robust show more differentially genes and a
"B" value around 50. The P.value was around 1E-016. This is OK?
Please, if you have a time, tell me how this method I use. Or I try they
and use how I like?
I have a single channel data set from filters (nylon membrane). Each
experiment have 6 biological repetition and each gene is printed 2 times
in each filter. I have one reference and 3 times points. I construct a
contrast matrix and do all constrast. I use topTable and heatDiagram to
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