[BioC] affxparser updateCelUnit question

[Henrik Bengtsson]

Hi,

if you are trying to write a vector of probe intensities to a CEL
file, and you have the corresponding probe indices, then use
updateCel(), e.g.

  updateCel(pathname, indices=idxs, intensities=y)

This does not require knowing the CDF structure.  (FYI, any function
with "unit" in its name, such as updateCelUnits(), utilizes a CDF
structure for its reading/writing.)

FYI, if the aroma.affymetrix package [http://www.aroma-project.org/]
provides a higher-level API on top of affxparser for dealing with
single or sets of CEL files.  It also provides a standard file
structure for hold data sets, so you/each person don't have to invent
their own each time.  ...and more.  You might find it useful.  If
you're developing custom preprocessing methods, they can be made so
they plug in transparently.

/Henrik

On Tue, Jul 12, 2011 at 6:59 AM, M Behnke <mkbehnke at gmail.com> wrote:
> 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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>
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