Does illuminaHumanv3BeadID.db correspond to the Illumina HT-12 chip
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@macartney-donia-3792
Last seen 10.6 years ago
Hi Sorry if I've missed this somewhere I'm analysing new data from an Human Illumina HT-12 v3 BeadChip. I'm using BeadID as the identifier however the illuminaHumanv3BeadID.db package seems to be missing some of the Bead Ids from my top table list. Is there a different package I can use - or what packages should I use to create my own annotation package? Many thanks Donia Session Info: R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_New Zealand.1252 LC_CTYPE=English_New Zealand.1252 LC_MONETARY=English_New Zealand.1252 LC_NUMERIC=C [5] LC_TIME=English_New Zealand.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] illuminaHumanv3BeadID.db_1.3.4 limma_3.2.1 lumi_1.12.0 MASS_7.3-3 [5] preprocessCore_1.8.0 mgcv_1.5-6 affy_1.24.0 annotate_1.24.0 [9] illuminaHumanv3.db_1.4.0 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 DBI_0.2-4 [13] AnnotationDbi_1.8.0 beadarray_1.14.0 Biobase_2.6.0 loaded via a namespace (and not attached): [1] affyio_1.14.0 grid_2.10.0 hwriter_1.1 lattice_0.17-26 nlme_3.1-96 tools_2.10.0 xtable_1.5-5 P Think before you print This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you. [[alternative HTML version deleted]]
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Matthew Ritchie ▴ 1000
@matthew-ritchie-650
Last seen 11 months ago
Australia
Dear Donia, > Sorry if I've missed this somewhere > > I'm analysing new data from an Human Illumina HT-12 v3 BeadChip. I'm using > BeadID as the identifier however the illuminaHumanv3BeadID.db package > seems to be missing some of the Bead Ids from my top table list. Is there > a different package I can use - or what packages should I use to create my > own annotation package? You are using the correct package. Note that this annotation package (and most others available from BioC) only contains information for non- control probes. Maybe the probes in question are controls? You can get a list of control BeadIDs for Human v3 chips using the following commands - check to see whether any of these match up with the ones in your top table. library(beadarray) data(ExpressionControlData) ExpressionControlData$Humanv3[,1] I hope this helps. Best wishes, Matt
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Dear Matt Thanks for replying quickly. I don't think (hope) I haven't done anything dumb.... but I checked controls against my toptable and they didn't overlap. So I definitely have some non-control probes that are missing from the annotation package. I've also looked at the number of probes in my array data and I have 48,803, and this matches the number in the HT-12 annotation file from Illumina (I'll send you a copy). So I guess the information used to create the annotation file was different. How do I go about creating my own annotation package? Many thanks for you help Best wishes Donia -----Original Message----- From: Matthew Ritchie [mailto:mritchie@wehi.EDU.AU] Sent: Wednesday, 11 November 2009 1:57 p.m. To: Macartney, Donia Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Does illuminaHumanv3BeadID.db correspond to the Illumina HT-12 chip Dear Donia, > Sorry if I've missed this somewhere > > I'm analysing new data from an Human Illumina HT-12 v3 BeadChip. I'm > using BeadID as the identifier however the illuminaHumanv3BeadID.db > package seems to be missing some of the Bead Ids from my top table > list. Is there a different package I can use - or what packages should > I use to create my own annotation package? You are using the correct package. Note that this annotation package (and most others available from BioC) only contains information for non-control probes. Maybe the probes in question are controls? You can get a list of control BeadIDs for Human v3 chips using the following commands - check to see whether any of these match up with the ones in your top table. library(beadarray) data(ExpressionControlData) ExpressionControlData$Humanv3[,1] I hope this helps. Best wishes, Matt P Think before you print This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you.
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Hi, Thanks for the report. Along with the control probes, we also discard anything that is poorly annotated on the array (see our website:- http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html) However, on this occasion I think there are more probes missing than I would expect. I'll have to check the input to the annotation packages and re-build if necessary. Regards, Mark On Wed, Nov 11, 2009 at 5:07 AM, Macartney, Donia <donia.macartney at="" esr.cri.nz=""> wrote: > Dear Matt > > Thanks for replying quickly. > > I don't think (hope) I haven't done anything dumb.... > > but > > I checked controls against my toptable and they didn't overlap. So I definitely have some non-control probes that are missing from the annotation package. > > I've also looked at the number of probes in my array data and I have 48,803, and this matches the number in the HT-12 annotation file from Illumina (I'll send you a copy). So I guess the information used to create the annotation file was different. > > How do I go about creating my own annotation package? > > Many thanks for you help > > Best wishes > > Donia > > > > -----Original Message----- > From: Matthew Ritchie [mailto:mritchie at wehi.EDU.AU] > Sent: Wednesday, 11 November 2009 1:57 p.m. > To: Macartney, Donia > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Does illuminaHumanv3BeadID.db correspond to the Illumina HT-12 chip > > Dear Donia, > >> Sorry if I've missed this somewhere >> >> I'm analysing new data from an Human Illumina HT-12 v3 BeadChip. I'm >> using BeadID as the identifier however the ?illuminaHumanv3BeadID.db >> package seems to be missing some of the Bead Ids from my top table >> list. Is there a different package I can use - or what packages should >> I use to create my own annotation package? > > You are using the correct package. ?Note that this annotation package (and most others available from BioC) only contains information for non-control probes. ?Maybe the probes in question are controls? ?You can get a list of control BeadIDs for Human v3 chips using the following commands - check to see whether any of these match up with the ones in your top table. > > library(beadarray) > data(ExpressionControlData) > ExpressionControlData$Humanv3[,1] > > I hope this helps. ?Best wishes, > > Matt > > > P Think before you print > This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. > If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Mark Dunning ★ 1.1k
@mark-dunning-3319
Last seen 21 days ago
Sheffield, Uk
Hi Donia, I checked the IDs you sent me off the BioC list. All except two are classed as "Bad" by our recent re-annotation of the platform, meaning they are unlikely to accurately measure the target that they were designed for. You can search such details at our website http://remoat.sysbiol.cam.ac.uk/ The other two IDs have no RefSeq symbol associated so will not be annotated. Nevertheless, I did find some probes that were missing from the annotation package that should not have been, so I will be uploading a new version to BioC very soon. Regards, Mark >>> -----Original Message----- >>> From: Matthew Ritchie [mailto:mritchie at wehi.EDU.AU] >>> Sent: Wednesday, 11 November 2009 1:57 p.m. >>> To: Macartney, Donia >>> Cc: bioconductor at stat.math.ethz.ch >>> Subject: Re: [BioC] Does illuminaHumanv3BeadID.db correspond to the >>> Illumina HT-12 chip >>> >>> Dear Donia, >>> >>>> Sorry if I've missed this somewhere >>>> >>>> I'm analysing new data from an Human Illumina HT-12 v3 BeadChip. I'm >>>> using BeadID as the identifier however the ?illuminaHumanv3BeadID.db >>>> package seems to be missing some of the Bead Ids from my top table >>>> list. Is there a different package I can use - or what packages >>>> should I use to create my own annotation package? >>> >>> You are using the correct package. ?Note that this annotation package (and most others available from BioC) only contains information for non-control probes. ?Maybe the probes in question are controls? ?You can get a list of control BeadIDs for Human v3 chips using the following commands - check to see whether any of these match up with the ones in your top table. >>> >>> library(beadarray) >>> data(ExpressionControlData) >>> ExpressionControlData$Humanv3[,1] >>> >>> I hope this helps. ?Best wishes, >>> >>> Matt >>> >>> >>> P Think before you print >>> This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. >>> If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >
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