Hi,
the solution to this problem is to filter out the PCR fragments by
length that you wish the fragment-length normalization step should
utilize, e.g.
ds <- doASCRMAv2("MEFa_1", chipType="MOUSEDIVm520650", lengthRange=c(450,2000))
For more background, see:
[1] Post 'aroma.affymetrix v2.0.0 released' on 2011-02-18 [http://goo.gl/qb7ja]
[2] aroma.affymetrix' NEWS files
[http://cran.r-project.org/web/packages/aroma.affymetrix/NEWS]
[3] Thread 'Exception: Cannot fit normalization function to enzyme,
because there are no (finite) data points that are unique to this
enzyme: 1' on [http://goo.gl/PyMk6]
The latter explains the history and why it did not use to work.
Hope this helps
/Henrik
On Sat, Sep 24, 2011 at 4:17 AM, Rico.Daniel <dr...@cnio.es> wrote:
> Hello, I having problems trying to run CRMAv2 in two Affy Mouse arrays
> (MOUSEDIVm520650).
>
> I am using the files from http://aroma-project.org/chipTypes/MOUSEDIVm520650
> plus the CDF downloaded from Affymetrix. I believe that the files are in the
> correct directory structure, as I am able to run some of the inicial steps.
> But, when I try to run all, this is what I have:
>
>> ds <- doASCRMAv2("MEFa_1", chipType="MOUSEDIVm520650")
> Loading required package: sfit
> sfit v0.2.0 (2011-05-15) successfully loaded. See ?sfit for help.
> Error in list(`doASCRMAv2("MEFa_1", chipType = "MOUSEDIVm520650")` =
> <environment>, :
>
> [2011-09-24 12:55:26] Exception: Cannot fit normalization function, because
> none of the units are on fragments from a singl\
> e enzyme, or equivalently, there exist no rows in argument 'fragmentLenghts'
> that only have one finite value.
> at throw(Exception(...))
> at throw.default("Cannot fit normalization function, because none of the
> units
> at throw("Cannot fit normalization function, because none of the units are on
> at normalizeFragmentLength.default(y, fragmentLengths = fl, targetFcns =
> targe
> at normalizeFragmentLength(y, fragmentLengths = fl, targetFcns = targetFcns,
> s
> at process.FragmentLengthNormalization(fln, verbose = verbose)
> at process(fln, verbose = verbose)
> at doCRMAv2.AffymetrixCelSet(csR, ..., verbose = verbose)
> at doCRMAv2(csR, ..., verbose = verbose)
> at doCRMAv2.character(..., combineAlleles = FALSE)
> at doCRMAv2(..., combineAlleles = FALSE)
> at doASCRMAv2.default("MEFa_1", chipType = "MOUSEDIVm520650")
> at doASCRMAv2("MEFa_1", chipType = "MO
> In addition: There were 32 warnings (use warnings() to see them)
>> warnings()
> Warning messages:
> 1: In seek.connection(con, origin = "current", where = -5) :
> whence = "end" is not implemented for gzfile connections
> 2: In seek.connection(con, origin = "current", where = -5) :
> whence = "end" is not implemented for gzfile connections
> 3: In seek.connection(con, origin = "current", where = -5) :
> whence = "end" is not implemented for gzfile connections
> 4: In seek.connection(con, origin = "current", where = -5) :
> whence = "end" is not implemented for gzfile connections
>
> Here is my sessionInfo:
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] sfit_0.2.0 aroma.affymetrix_2.2.0 affxparser_1.24.0
> [4] aroma.apd_0.2.0 R.huge_0.3.0 aroma.cn_0.8.2
> [7] aroma.core_2.2.0 aroma.light_1.20.0 matrixStats_0.2.2
> [10] R.rsp_0.6.2 R.filesets_1.1.0 digest_0.5.0
> [13] R.cache_0.5.1 R.utils_1.7.8 R.oo_1.8.1
> [16] R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
> [1] splines_2.13.0 tools_2.13.0
> Warning message:
> 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
>
>
> Any help from someone who had analyzed this type of arrays would be greatly
> appreciated!!
>
> Thanks a lot,
> Daniel
>
> ********************************************
>
> Daniel Rico Rodriguez, PhD.
> Structural Biology and BioComputing Programme
> Spanish National Cancer Research Center, CNIO
> Melchor Fernandez Almagro, 3.
> 28029 Madrid, Spain.
> Phone: +34 91 224 69 00 #3015
> dr...@cnio.es
> http://www.cnio.es
>
> ********************************************
>
>
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version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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