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 > > ******************************************** > > > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los > ficheros adjuntos, pueden contener información protegida para el uso > exclusivo de su destinatario. 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