[BioC] farms package fails on estrogen data

Javier Pérez Florido jpflorido at gmail.com
Tue Mar 16 16:25:42 CET 2010

Dear list,
I've tried to use l.farms (farms package)
for preprocessing the estrogen data set available at

When trying to preprocess using l.farms, the following error comes up:

background correction: none
normalization: loess
PM/MM correction : pmonly
expression values: farms
background correcting...done.
normalizing...Error: NA/NaN/Inf in call to external function (arg 1)

q.farms works for the same data set and l.farms works for the Dilution 
data set, so, I don't know what is going on here.

Any suggestions?

R version 2.10.1 (2009-12-14)

[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] affyPLM_1.22.0       preprocessCore_1.8.0 gcrma_2.18.1
[4] affydata_1.11.10     farms_1.4.0          MASS_7.3-4
[7] hgu95av2cdf_2.5.0    affy_1.24.2          Biobase_2.6.1

loaded via a namespace (and not attached):
[1] affyio_1.14.0      Biostrings_2.14.12 IRanges_1.4.11     splines_2.10.1
[5] tools_2.10.1

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