Yes, it should be alright to those annotation data files I've placed on
http://aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/ The attached plot is a proof of concept using an example data set from Affymetrix. FYI, *.acs (and *.ugp, and *.ufl) files are binary files, so I doubt 'wc' is inappropriate to use. Instead you can use, say, readSequences(acs, cells=1010:1015) to retrieve the probe sequences and hence compare them with those of another file. /Henrik On Thu, Jan 12, 2012 at 11:23 PM, D Goode <dgoode.stanf...@gmail.com> wrote: > Sorry Henrik, missed your post from last week. I downloaded your acs file. > It's the same size and the number of rows appear to be the same as the one > I made (as determined by aroma), but there appear to have differences in > file structure: > > dgoode$ wc CytoScanHD_Array,HB20111008.acs > 11 21 179217487 CytoScanHD_Array,HB20111008.acs > > dgoode$ wc CytoScanHD_Array,HB20111008.acs > 2 11 179217220 > annotationData/chipTypes/old/CytoScanHD_Array,20120104.acs > > I'll try building the acs again. In the meantime, is it safe to use yours? > > Cheers, > David > > > On Friday, 13 January 2012 15:55:25 UTC+11, Henrik Bengtsson wrote: >> >> Ok, so it fails to identify any SNP positions based on your ACS file, cf. >> >> > SNP positions: >> > int [1:2410205] NA NA NA NA NA NA NA NA NA NA ... >> > Tabulated SNP positions: >> > character(0) >> > Unique SNP positions: >> > integer(0) >> >> My guess is that your ACS file is incorrect (all zeros?). Did you >> compare ("validate") your ACS file to that of mine, as I suggested in >> thread 'Using aroma with Cytoscan HD array data' on Jan 6, 2012: >> >> https://groups.google.com/forum/#!topic/aroma-affymetrix/oDS9ItjkqnY >> >> /Henrik >> >> > -- > 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/
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