[BioC] lmFit and topTable

[Jenny Drnevich]

Hi Tiandao,

You seem to only be following the vignette without checking to see if 
the code it uses is appropriate for your data. In addition to the 
vignette, you should read through the help page for each main 
function for more information on the options/arguments available and 
what the different choices mean. For example, checking 
?duplicateCorrelation shows that there is an argument called 
"spacing" with a default value of 1. The description of spacing: the 
spacing between the rows of object corresponding to duplicate spots, 
spacing=1 for consecutive spots.  Are all 4 of your duplicate spots 
right after each other? Probably not, else you would not be getting 
duplicate gene names in your output. If the spots do not have a 
consistent spacing between them, you can sort your g2 object (after 
all pre-processing and normalization) so that they are in consecutive 
order. You'll have to be careful about blanks & buffers, or other 
spots that may show up >4 times.


>Another question, is there any difference between methods of "ls" and
>"robust" in lmFit?

Of course there is a difference! Read through the entire help page of 
lmFit, and the links from there for more information.

Cheers,
Jenny



> > sessionInfo()
>R version 2.6.0 (2007-10-03)
>i486-pc-linux-gnu
>
>locale:
>LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
>attached base packages:
>[1] stats     graphics  grDevices utils     datasets  methods   base
>
>other attached packages:
>[1] MASS_7.2-37   statmod_1.3.1 limma_2.12.0
>
>loaded via a namespace (and not attached):
>[1] rcompgen_0.1-15
>
>Best wishes,
>
>Tiandao
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu