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/
