What is the name of your custom CDF, and what does print(cdf) report after loading it with cdf <- AffymetrixCdfFile$byName(...)?
/Henrik On Wed, May 4, 2011 at 3:56 PM, Fong <fongchunc...@gmail.com> wrote: > Hi all, > > I've created a customCDF following the procedure listed at: > http://www.aroma-project.org/node/40 > > The customCDF I made was based on the Brainarray group CDF (ense14 for > Human Exon arrays to be exact). I wanted to create a CDF which I > could run FIRMA on since the customCDF provided by the BrainArray > doesn't appear map the probeset (group ids) onto the appropriate gene > (unit IDs) which is necessary to run FIRMA. I create one that works > in the flat2CDF() script provided by aroma.affymetrix and then when I > used it on aroma affymetrix I got the following error: > > 20110504 15:46:17| Setting up ExonChipEffectFile...done > 20110504 15:46:17| Retrieving chip-effect #19 of 20 (8_4N)...done > 20110504 15:46:17| Retrieving chip-effect #20 of 20 (9_5T)... > 20110504 15:46:17| Setting up ExonChipEffectFile... > 20110504 15:46:17| Pathname: plmData/ > gardina_colon_cancer,ense14,QN,RMA,merged/HuEx-1_0-st- > v2/9_5T,chipEffects.CEL > 20110504 15:46:17| Setting up ExonChipEffectFile...done > 20110504 15:46:17| Retrieving chip-effect #20 of 20 (9_5T)...done > 20110504 15:46:17| Retrieving chip-effects from data set...done > 20110504 15:46:17| Getting chip-effect set from data set...done > 20110504 15:46:17| Updating ExonChipEffectSet... > 20110504 15:46:17| Scanning for and applying sample annotation > files... > 20110504 15:46:17| Defining 0 files... > > 20110504 15:46:17| Defining 0 files...done > 20110504 15:46:17| No sample annotation files found. > 20110504 15:46:17| Scanning for and applying sample annotation > files...done > 20110504 15:46:17| Updating ExonChipEffectSet...done > 20110504 15:46:17| Identifying non-fitted units in chip-effect > file... > 20110504 15:46:17| Pathname: plmData/ > gardina_colon_cancer,ense14,QN,RMA,merged/HuEx-1_0-st- > v2/9_5T,chipEffects.CEL > 20110504 15:46:17| Found indices cached on file > 20110504 15:46:17| Reading data for these 442179 cells... > Error in readCel(getPathname(this), indices = idxs, readIntensities = > FALSE, : > Argument 'indices' is out of range [1,308580]. > Calls: fit ... findUnitsTodo -> findUnitsTodo.ChipEffectFile -> > readCel > 20110504 15:46:17| Reading data for these 442179 cells...done > 20110504 15:46:17| Identifying non-fitted units in chip-effect > file...done > 20110504 15:46:17| Identifying non-estimated units...done > 20110504 15:46:17|Fitting model of class ExonRmaPlm...done > > Has anyone run into this error before? Any ideas on what I am doing > wrong? > > Thanks, > > Fong > > -- > 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/ > -- 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/
