Hi. The Aroma Cell Sequence (ACS) file does not have to be updated, since it only contains the probe sequences on the array and those never changes.
The Unit Genome Position (UGP) file specifies the (chr, pos) genomic coordinates for the probe sets, which depends on the genome reference/build. Likewise, the Unit Fragment Length (UFL) file specify the PCR fragment lengths as cut by the restriction enzyme (part of the Affymetrix assay). These cut locations also depend on the genome reference/build. So, yes, UGP and UFL files needs to match the genome build wanted. (However, I wouldn't expect much any major/noticeable difference in CN estimates if not perfect version matching since not too much have changed and most discrepancies would come through as a few number outliers). To build newer versions yourself, please see how-to docs: * Create a Unit Genome Position (UGP) files * Create a Unit Fragment Length (UFL) files available via http://aroma-project.org/howtos/ Hope this helps Henrik On Thu, Jan 8, 2015 at 5:44 AM, Chengyu Liu <chengyu.liu...@gmail.com> wrote: > Hi, > > Is it necessary to update annotation files in > http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/. > It is quite old. Or I can use them without update. > > Br, > C.Y > > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
