User: Lynn Amon

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Lynn Amon280
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Posts by Lynn Amon

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Newbie Illumina Probe Annotation (beadarray) Problem
... One of the problems is that Illumina has changed the format of its identifiers. Perhaps the illuminaMousev1p1.db package should be changed to use the "ILMN_" type identifiers. Lynn Amon Priscila Darakjian wrote: > Actually, I would look at MouseRef-8_V1_1_R3_11234312_A.bgx (this probably has ...
written 10.1 years ago by Lynn Amon280
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Answer: A: Illumina annotation problem - illuminaHumanv2GENENAME
... Use illuminaHumanv2BeadID.db instead. You might want to take the one from the devel version instead of the release version as there were some problems with the initial package. Lynn McClellan, Elizabeth Ann wrote: > Dear Users, > > I have summarized data from an Illumina Human-6 v2 array ...
written 10.3 years ago by Lynn Amon280
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Answer: A: Illumina annotation packages discrepancy
... You can match the Array_Address_Id in the bead manifest file to the probe ID in the annotation package. Lynn Renaud Gaujoux wrote: > Ok. > Since I only have the summarized data I guess I cannot get back the > ids from the scanner (?) > For the moment I combine the data from the new lumi ...
written 10.3 years ago by Lynn Amon280
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Comment: C: Illumina annotation packages discrepancy
... You'll want to use the illuminaHumanv2ProbeID.db package. Lynn Renaud Gaujoux wrote: > Oups... I'm really sorry Mark for the confusion. I think misread the > vignette. > > I BLASTed some of the missing probes and some of them gave quite > convincing results (100% identity but with di ...
written 10.3 years ago by Lynn Amon280
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Comment: C: Illumina annotation packages discrepancy
... The illuminaHumanv2.db package is not a "proprietary" package. It is currently maintained by Mark Dunning (Mark.Dunning at cancer.org.uk). It is based on BLASTed sequences but there was a problem in creating the package when more than one accession was assigned to a probe which caused the annotatio ...
written 10.3 years ago by Lynn Amon280
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Comment: C: BMP4 probe '1940386' missing in illuminaHumanv2BeadID.db (as compared to illumin
... Julian, I no longer maintain the Illumina annotation packages but I can tell you that I made the illuminaHumanv2ProbeID.db package using annotation provided by Nuno Barbosa-Morais who BLASTed the probe sequences against hg18. I only used probes which had 100% similarity with refseq sequences. You ...
written 10.4 years ago by Lynn Amon280
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Comment: C: Bug in getOntoly-function (package annotate)?
... Hi Jukka, The annotation package you are using really should be updated. The current version is illuminaHumanv2ProbeID.db and as the name indicates uses the Probe ID as the identifier as was used in illuminaHumanBCv2. Please use this new package. Lynn Jukka Hiissa wrote: > Hi Marc and thanks f ...
written 10.5 years ago by Lynn Amon280
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Answer: A: illumina annotation packages vs. bgx manifests
... Hi Mikal, Okay, so first, use the more recent illuminaRatv1ProbeID.db package instead of illuminaRatBCv1. Secondly, I only included probes which mapped to RefSeq identifiers rather than those which could only be mapped to GenBank. So, if you found something in the .bgx file which maps to a gene sy ...
written 10.7 years ago by Lynn Amon280
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Answer: A: illumina annotation packages vs. bgx manifests
... Hi Michal, I'm not completely certain what you are asking. The Array_Address_ID is the probe identifier used in the illuminaRatv1ProbeID.db annotation package so you should link using that identifier. If you are going to use the .bgx file for annotation, you don't really need an annotation package ...
written 10.7 years ago by Lynn Amon280
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confusion about nomenclature of illumina annotationpackages
... Hi Paul, I used BLAST results for the 2006 Mouse assembly (mm8) from a group at Cambridge. http://www.compbio.group.cam.ac.uk/Resources/Annotation/ The ACCNUM part of the annotation package is what I used to search NCBI. I only searched probes which had 100% similarity with RefSeq nucleotides. For ...

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Popular Question 10.1 years ago, created a question with more than 1,000 views. For are older versions of Ensembl accessible with biomaRt?

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