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. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
