Thanks all, I knew that skipping them 'worked' but it is nice to know that this is the right thing to do.
On Mar 9, 2009, at 3:48 AM, Markus Ringnér wrote: > Pawel Sztromwasser wrote: >> We experienced that as well. I believe that I have checked these >> probes >> and they were controls, so they can be ignored. >> > > All of them are not necessarily controls since the number of probes > missing in the bgx-files may change between Illumina revisions of > bgx-files. Our interpretation is that some probes that used to be > annotated with a gene has later been considered poor by Illumina > (as we > have only observed an increase in the number of unmatched probes for > later bgx revisions). > > Importantly, if you follow Nicklas's 'Probe not found=skip' > recommendation, you will get the same number of probes (and the same > probes) as when using BeadStudio (BeadStudio silently ignores the > probes > not in the bgx-files; you also end up with slightly different > numbers of > probes in BeadStudio for different bgx revisions). > > Markus > >> Pawel >> >> Nicklas Nordborg wrote: >>> David Waring wrote: >>>> I have recently installed the Illumina Plugins and have imported >>>> features for several Array Designs. We modified our config to >>>> generate the Bead Summary files and I have imported the data. Oddly >>>> have found that the Bead Summary files contain some rows with >>>> illumina codes that are not in the BGX files. For example the >>>> datasets from HumanRef-8 arrays contain 324 probes that are not >>>> found >>>> in any of the various versions of BGX files are available from the >>>> Illumina web site. If I run these same datasets through BeadStudio >>>> these these probes are not found in the BeadStudio output. >>>> >>>> Has anyone else run into this situation? >>> Yes, we have seen this also. Just select 'Probe not found=skip' when >>> importing the data to BASE and everything should work. >>> >>> /Nicklas >>> >>> -------------------------------------------------------------------- >>> ---------- >>> Open Source Business Conference (OSBC), March 24-25, 2009, San >>> Francisco, CA >>> -OSBC tackles the biggest issue in open source: Open Sourcing the >>> Enterprise >>> -Strategies to boost innovation and cut costs with open source >>> participation >>> -Receive a $600 discount off the registration fee with the source >>> code: SFAD >>> http://p.sf.net/sfu/XcvMzF8H >>> _______________________________________________ >>> basedb-devel mailing list >>> basedb-devel@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/basedb-devel >> >> >> --------------------------------------------------------------------- >> --------- >> Open Source Business Conference (OSBC), March 24-25, 2009, San >> Francisco, CA >> -OSBC tackles the biggest issue in open source: Open Sourcing the >> Enterprise >> -Strategies to boost innovation and cut costs with open source >> participation >> -Receive a $600 discount off the registration fee with the source >> code: SFAD >> http://p.sf.net/sfu/XcvMzF8H >> _______________________________________________ >> basedb-devel mailing list >> basedb-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/basedb-devel > > ---------------------------------------------------------------------- > -------- > Open Source Business Conference (OSBC), March 24-25, 2009, San > Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the > Enterprise > -Strategies to boost innovation and cut costs with open source > participation > -Receive a $600 discount off the registration fee with the source > code: SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > basedb-devel mailing list > basedb-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/basedb-devel ------------------------------------------------------------------------------ Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
