Hi, see Vignette 'Estimation of total copy numbers using the CRMA v2 method (10K-6.0)' under
http://groups.google.com/group/aroma-affymetrix/web /Henrik PS. It helps us to help you if you let us know where you got your script from. On Tue, Sep 1, 2009 at 2:55 AM, sachin<krsac...@gmail.com> wrote: > > Hi all, > > I am new to this area and just stated to use aroma.affymetrix for CGH > array analysis. > > I got error while doing analysis... I thought its because of SNP INFO > file but I am not sure. I am using snp info file from dChip > (snp6.0_genome_info file) and this file does not contain few > information like fragment length. > > Here is the error of analysis:- > ----------------------------------------------------------------------------------------------------------------------------------------------- >> si <- getSnpInformation(cdf) >> ces <- getChipEffectSet(plm) >> fln <- FragmentLengthNormalization(ces) >> cesN <- process(fln, verbose=TRUE) > > Normalizing set for PCR fragment-length effects... > Identifying SNP and CN units... > types > 1 2 5 > 621 909622 945826 > subsetToUpdate: > int [1:1855448] 622 623 624 625 626 627 628 629 630 631 ... > Identifying SNP and CN units...done > Retrieving SNP information annotations... > DChipSnpInformation: > Name: GenomeWideSNP_6 snp info > Tags: > Full name: GenomeWideSNP_6 snp info > Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6 > snp info.txt > File size: 34.55 MB (36228348 bytes) > RAM: 0.00 MB > Chip type: GenomeWideSNP_6 > Number of enzymes: 1 > Retrieving SNP information annotations...done > Identifying the subset used to fit normalization function(s)... > Error in list(`process(fln, verbose = TRUE)` = <environment>, > `process.FragmentLengthNormalization(fln, verbose = TRUE)` = > <environment>, : > > [2009-08-31 20:04:11] Exception: Failed to retrieve genome information > for this chip type: GenomeWideSNP_6 > at throw(Exception(...)) > at throw.default("Failed to retrieve genome information for this > chip type: ", chipType) > at throw("Failed to retrieve genome information for this chip type: > ", chipType) > at getGenomeInformation.AffymetrixCdfFile(cdf) > at getGenomeInformation(cdf) > at getSubsetToFit.FragmentLengthNormalization(this, verbose = less > (verbose)) > at getSubsetToFit(this, verbose = less(verbose)) > at process.FragmentLengthNormalization(fln, verbose = TRUE) > at process(fln, verbose = TRUE) > Identifying the subset used to fit normalization function(s)...done > Normalizing set for PCR fragment-length effects...done > ------------------------------------------------------------------------------------------------------------------------------------------------------------ > > I just paste the error above not the whole analysis code. > If its error because of SNP info file for GenomeWideSNP6 chip type, > then from where to get the correct snp info file. > Could somebody please help me out. > > regards > sachin > > > > --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
