Re: [basedb-devel] Illumina Bead Summary Files
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
Re: [basedb-devel] Illumina Bead Summary Files
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
Re: [basedb-devel] Illumina Bead Summary Files
We experienced that as well. I believe that I have checked these probes and they were controls, so they can be ignored. 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
Re: [basedb-devel] Illumina Bead Summary Files
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
[basedb-devel] Illumina Bead Summary Files
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? -- 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
