[BioC] RMA and justRMA error

[Ben Bolstad]

Typically, when I have encountered others who have had this error occur
it is because they have corrupted data. For instance this piece of
demonstration code will generate the same error:


library(affy);library(affydata)
data(Dilution)
Dilution.Corrupted <- Dilution
pm(Dilution.Corrupted)[1,1] <- 30000000  
# that is an extreme value outside the
# range of normal raw probe intensities

eset <- rma(Dilution.Corrupted)


My suggestion would be to examine things along those lines.

Best,

Ben








On Tue, 2006-08-15 at 15:01 -0400, aedin wrote:
> Dear BioC
> I know that this error is reported a few times on the Bioc mailing list, 
> however no resolution to it is available in the archives (or at least 
> none that google and I could find).  I get the same error whether I use 
> R 2.3.1 or the devel version.  I enclose the devel version error.
> 
> The cels files are read in by ReadAffy and are processed ok by gcrma, 
> however fall over when I try to run rma or justRMA.
> 
> Thanks for your help
> Aedin
> 
>  > df = justRMA(filenames=filenam[125:130])
> Background correcting
> Error in density.default(x, kernel = "epanechnikov", n = 2^14) :
>         need at least 2 points to select a bandwidth automatically
> 
>  > df = ReadAffy(filenames=filenam[125:130])
>  > df
> AffyBatch object
> size of arrays=1164x1164 features (63518 kb)
> cdf=HG-U133_Plus_2 (54675 affyids)
> number of samples=6
> number of genes=54675
> annotation=hgu133plus2
> 
>  > df.rma= rma(df)
> Background correcting
> Error in density.default(x, kernel = "epanechnikov", n = 2^14) :
>         need at least 2 points to select a bandwidth automatically
> 
>  > library(gcrma)
>  > df.gcrma= gcrma(df)
> Adjusting for optical effect......Done.
> Computing affinities.Done.
> Adjusting for non-specific binding......Done.
> Normalizing
> Calculating Expression
> 
>  > sessionInfo()
> R version 2.4.0 Under development (unstable) (2006-08-06 r38809)
> i686-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] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
> [7] "utils"     "datasets"  "base"
> 
> other attached packages:
> hgu133plus2probe   hgu133plus2cdf            gcrma      matchprobes
>         "1.12.0"         "1.12.0"          "2.5.1"          "1.5.0"
>             affy           affyio          Biobase            made4
>         "1.11.6"          "1.1.5"        "1.11.24"          "1.7.1"
>    scatterplot3d             ade4
>         "0.3-24"          "1.4-1"

-- 
Ben Bolstad <bmb at bmbolstad.com>
http://bmbolstad.com