[BioC] farms package fails on estrogen data

[Martin Morgan]

On 03/16/2010 08:25 AM, Javier Pérez Florido wrote:
> Dear list,
> I've tried to use l.farms (farms package)
> http://www.bioinf.jku.at/software/farms/farms.html
> for preprocessing the estrogen data set available at
> http://www.bioconductor.org/packages/release/data/experiment/html/estrogen.html
> 
> 
> 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?

Hi Javier --

If I

  library(farms)
  library(estrogen)
  setwd(system.file("extdata", package="estrogen"))
  ab = ReadAffy()
  l.farms(ab)

I see the error you report. It is because

> sum(intensity(ab) == 0)
[1] 5

so that log transformation generates -Inf and then the error. It doesn't
seem too bad to

  intensity(ab) = 1 + intensity(ab)

[I don't know enough about the inner workings of affyio, but I'm
surprised that I sometimes see

> range(intensity(ReadAffy()))
[1]     0 46131

> range(intensity(ReadAffy))
[1] 1.563578e-316  4.613100e+04

suggesting either initialized memory or unanticipated 'empty' intensity
grid coordinates)]

Martin


> Javier
> 
> sessionInfo()
> R version 2.10.1 (2009-12-14)
> i386-pc-mingw32
> 
> locale:
> [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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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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