[BioC] Limma/Affy - Include expression Intensity in Final 'decideTests' results - limm2annaffy

[Steve Lianoglou]

Howdy,

On Tue, Apr 30, 2013 at 9:59 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
> Hi Atul,
>
> You might then try writeFit(), which is probably more to your liking.
> Something like
>
> write.table(writeFit(fit2, "mouse4302", esetRMA.Reduced), "All_data.txt",
> sep = "\t", quote=FALSE, row.names = FALSE)
>
> Also please note that Excel has an unfortunate habit of changing any gene
> symbol that looks like a date into a date, and this is irreversible (so
> e.g., the 1Apr gene will be converted to 4/1/2013, because that makes
> sense...).

Tim had previously pointed my attention to this package:
http://cran.r-project.org/web/packages/HGNChelper/index.html

which has a function called `findExcelGeneSymbols` with the following
description:

"""
This function identifies gene symbols which may have been
mogrified by Excel or other spreadsheet programs.  If output is
assigned to a variable, it returns a vector of the same length
where symbols which could be mapped have been mapped.
"""

I've never used it, so I'm not sure how well it works or not -- I
mean, I wouldn't trust it, but gotta give credit to the author for
trying :-)

-steve

--
Steve Lianoglou
Computational Biologist
Department of Bioinformatics and Computational Biology
Genentech