Thanks very much, Henrik。Then I will not update these files. I will use the ones you provided. Now I am trying to get the pipeline working.
On Monday, January 12, 2015 at 11:47:17 PM UTC+2, Henrik Bengtsson wrote: > > 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/ > <http://www.google.com/url?q=http%3A%2F%2Faroma-project.org%2Fhowtos%2F&sa=D&sntz=1&usg=AFQjCNFzLVQVAza587qyuU3acW8gm18aoQ> > > > Hope this helps > > Henrik > > > On Thu, Jan 8, 2015 at 5:44 AM, Chengyu Liu <chengyu...@gmail.com > <javascript:>> 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-af...@googlegroups.com > <javascript:> > > 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-affymetr...@googlegroups.com <javascript:>. > > 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.
