Hello all,

I have normalized data from hgu133a2 microarray experiments using a custom
algorithm, in the format of a matrix with rowname=probe position and columns
the normalized intensity values for each sample (125 samples). I am trying
to write the data back out to individual CEL files using affxparser.  I
successfully created the 'empty' CEL files using createCel.  Because I only
have the PM probes, I believe I need to use the updateCelUnits function.
Following the vignette, I set up my code for the first sample as such (CDF
file is in the working directory):

pathname <- file.path(getwd(), basename(files[1]))
intens=as.list(normed.1[,1])
updateCelUnits(pathname, cdf=NULL, intens)
and checked my variables-
> pathname
[1] "L:/Normed data/CIR_5-D-309.CEL"

> intens[1:4]
$`129981`
[1] 7.566183
$`212118`
[1] 8.783549
$`393384`
[1] 8.812677
$`84268`
[1] 10.39683
However, when I run the function I get the following error:
> updateCelUnits(pathname, cdf=NULL, intens)
Error in dirname(filename) : a character vector argument expected
> is.character(pathname)
[1] TRUE
> is.vector(pathname)
[1] TRUE
Since I do appear to be giving it a character vector, I'm stumped.  Can
someone help?
My session info appears below.

Thank you very much!
Mikki Behnke
Doctoral Student
Virginia Commonwealth University

R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
 [1] affxparser_1.24.0          hgu133a2hsrefseq.db_14.1.0
 [3] org.Hs.eg.db_2.5.0         RSQLite_0.9-4
 [5] DBI_0.2-5                  AnnotationDbi_1.14.1
 [7] hgu133a2cdf_2.8.0          simpleaffy_2.28.0
 [9] gcrma_2.24.1               genefilter_1.34.0
[11] affy_1.30.0                Biobase_2.12.1
loaded via a namespace (and not attached):
[1] affyio_1.20.0         annotate_1.30.0       Biostrings_2.20.0
[4] IRanges_1.10.0        preprocessCore_1.14.0 splines_2.13.0
[7] survival_2.36-9       tools_2.13.0          xtable_1.5-6
>

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