[BioC] affxparser updateCelUnit question
Harris A. Jaffee
hj at jhu.edu
Wed Jul 13 20:21:17 CEST 2011
Your idxs seems to be of type character when it ought to be numeric,
at least when passed as the indices argument:
indices: A 'numeric' 'vector' of cell (probe) indices specifying which
cells to updated. If 'NULL', all indices are considered.
This should avoid the error:
idxs = as.numeric(rownames(normed.1))
On Jul 13, 2011, at 1:49 PM, M Behnke wrote:
> Hi,
> Thanks for the reply! I didn't think I could use updateCel since I
> only
> have the 247,899 PM values. I did try it though and something
> strange is
> happening:
>
> With this code:
> files=list.files(pattern="[.](CEL)$")
> names=colnames(normed.1)
>
> pathname <- file.path(getwd(), basename(files[1]))
> intens=(normed.1[,1])
> idxs=rownames(normed.1)
> updateCel(pathname,indices=idxs,intensities=intens)
>
> I get the error
> Error in updateCel(pathname, indices = idxs, intensities = intens) :
> Argument 'indices' is out of range [1,535824]: [1000,9999]
> Using debug, the error is occuring here:
> debug: if (r[1] < 1 || r[2] > nbrOfCells) {
> stop("Argument 'indices' is out of range [1,", nbrOfCells,
> "]: ", "[", r[1], ",", r[2], "]")
> }
>
> When I set up r as in the code with r=range(idxs), I do get
>> r
> [1] "1000" "9999"
> And
>> min(idxs)
> [1] "1000"
>> max(idxs)
> [1] "9999"
> BUT, random sampling of idxs shows values outside that range -
>> idxs[45]
> [1] "57961"
>>> idxs[9000]
> [1] "46169"
> I may well be making a basic programming error, as I am apparently
> a much
> better molecular biologist than I am a programmer! Any help you
> can give
> would be much appreciated!
>
> I will also check out aroma.affymetrix as you suggest.
>
> thanks again,
> Mikki
> On Wed, Jul 13, 2011 at 12:31 PM, Henrik Bengtsson
> <hb at biostat.ucsf.edu>wrote:
>
>> 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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