Question

Annotation DB for ArrayStar lncRNA arrays

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Kevin Coombes ▴ 430

@kevin-coombes-3935

Last seen 18 months ago

United States

I'm helping someone analyze array data from the ArrayStar lncRNA 2.0 microarrays. The company claims that they can't or won't provide annotations for every probe on the array, since that information is proprietary. They will only provide it for probes that they found to be differentially expressed in their own analyses based on things you asked them to contrast when you initially purchased the array service from them.

However, the company has created two platform description files in GEO (GPL13825 and GPL15314) that contain the full sequences of the probes they are using. Presumably, someone could BLAST those sequences agaiunst the genome and then create their own set of annotations.

Question 1: Has anyone used the ArrayStar GPL files to construct their own annotation database? If so, can you supply a copy?

Question 2: Is anyone interested in helping put together such an annotation database and contributing it to BioConductor?

arraystar lncRNA annotation annotationdbi • 3.1k views

ADD COMMENT • link updated 8.7 years ago by xiangy7 • 0 • written 9.1 years ago by Kevin Coombes ▴ 430

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What exactly do you mean by annotate? Just mapping the ArrayStar IDs to the Broad's lincRNA IDs? Adding in some other stuff they have here?

ADD REPLY • link 9.1 years ago James W. MacDonald 65k

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Actually it would be nice to use ENSEMBL/lncipedia mappings. From my experience they are the most useful. Maybe dr Coombes has observations to the contrary but I've looked at the OSU lncRNA array data and mapping those IDs was not easy! I think I know exactly which dataset is pissing you off, in fact. :-) I would be interested in doing this and have used seqmap for it in the recent past (for other purposes) Id also be interested in making sure fRMA or scan.upc works with the resulting reannotations Best of all I now have some people working for me so I might even have time to dig through my old code and make it not suck so much This could possibly be done in time for the next release. You all know how to reach me by email if interested. I think it is a hole worth filling, especially if you are at tOSU or UNSW. Just saying ;-) Best, --t > On Mar 18, 2015, at 10:48 AM, James W. MacDonald [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > User James W. MacDonald wrote Comment: Annotation DB for ArrayStar lncRNA arrays: > > What exactly do you mean by annotate? Just mapping the ArrayStar IDs to the Broad's lincRNA IDs? Adding in some other stuff they have here? > > You may reply via email or visit C: Annotation DB for ArrayStar lncRNA arrays

ADD REPLY • link 9.1 years ago Tim Triche ★ 4.2k

score 0 · Answer 1 · 2015-08-26

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xiangy7 • 0

@xiangy7-8685

Last seen 8.7 years ago

China

Hello，Dr.Coombes, I am analyzing data based on ArryStar LncRNA 2.0 microarrays too and have the same trouble with u. Have u solved it yet?

ADD COMMENT • link 8.7 years ago xiangy7 • 0