[BioC] limma normalizeWithinArrays method="control"

Al Ivens alicat at sanger.ac.uk
Mon Jul 2 16:31:46 CEST 2007


I have a kooperberg bg subtracted object of 5 arrays that I am
subsequently trying to normalize for some hybridised spike samples.

The rownames of data for the spike probes (2000 of them, 37632 total
probes on the array) are stored as a vector:
> reserved[1:10]
 [1] 173 174 175 176 177 178 179 180 181 182

> KNWAspike <-

Error in simpleLoess(y, x, w, span, degree, parametric, drop.square,
normalize,  : 
        NA/NaN/Inf in foreign function call (arg 1)

If I add weights=NULL to the above command, it works.  Does this say
there is something wrong with one/more of my data points, or are the two
options (controlspots, weights) mutually exclusive?  I'd kinda like to
keep/use the weights.

Many thanks in advance for any suggestions!



> sessionInfo()
R version 2.5.0 (2007-04-23) 

LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices"
[6] "utils"     "datasets"  "methods"   "base"     

other attached packages:
geneplotter    annotate  genefilter    survival     Biobase 
   "1.14.0"    "1.14.1"    "1.14.1"      "2.32"    "1.14.0" 
     gplots       gdata      gtools     lattice        MASS 
    "2.3.2"     "2.3.1"     "2.3.1"   "0.15-11"    "7.2-34" 
    statmod         sma       limma       Hmisc 
    "1.3.0"    "0.5.15"    "2.10.0"     "3.4-1" 

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