Question

annotation of hgu133a

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Weiwei Shi ★ 1.2k

@weiwei-shi-1407

Last seen 9.7 years ago

Dear listers: I recently analyzed a dataset using u133a and happened to find the following poster: http://www.healthtech.com/2004/mda/Probe%20ID%20poster1.pdf I identified 22283 probesets from hgu133a and it was said in the poster that over 6000 of them needs to be updated. What do you think of it? Should a new annotation package be built for this? thanks, Weiwei -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Annotation hgu133a Annotation hgu133a • 914 views

ADD COMMENT • link updated 17.1 years ago by Sean Davis 21k • written 17.1 years ago by Weiwei Shi ★ 1.2k

score 0 · Answer 1 · 2007-04-17

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Sean Davis 21k

@sean-davis-490

Last seen 4 months ago

United States

Weiwei Shi wrote: > Dear listers: > > I identified 22283 probesets from hgu133a and it was said in the > poster that over 6000 of them needs to be updated. > > What do you think of it? Should a new annotation package be built for > this? Hi, Weiwei. I didn't look closely at the poster, but this has already been done. See here: http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/cdf readme.htm The answer to your question depends on what you mean by "updated". The annotation is redone every 6 months (approximately) based on information supplied by Affymetrix. If you choose to use annotation different from Affymetrix, it is probably a good idea to understand how the annotation (both from affy and the alternative) is produced in some detail so that you can weigh out the benefits of each. Sean

ADD COMMENT • link 17.1 years ago Sean Davis 21k

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Hi, Sean: I read the poster closely and felt they seemed to believe there were some errors there (i apologize if I am wrong). I already sent an email to ask for their annotation and am going to try both. thanks for the linky and it helps. Weiwei On 4/17/07, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > Weiwei Shi wrote: > > Dear listers: > > > > I identified 22283 probesets from hgu133a and it was said in the > > poster that over 6000 of them needs to be updated. > > > > What do you think of it? Should a new annotation package be built for > > this? > Hi, Weiwei. I didn't look closely at the poster, but this has already > been done. See here: > > http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/c dfreadme.htm > > The answer to your question depends on what you mean by "updated". The > annotation is redone every 6 months (approximately) based on information > supplied by Affymetrix. If you choose to use annotation different from > Affymetrix, it is probably a good idea to understand how the annotation > (both from affy and the alternative) is produced in some detail so that > you can weigh out the benefits of each. > > Sean > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

ADD REPLY • link 17.1 years ago Weiwei Shi ★ 1.2k

score 0 · Answer 2 · 2007-04-18

On Wednesday 18 April 2007 11:12, Weiwei Shi wrote: > Yes, I agreed with that. Then my next question, is there a way to > improve the probe design so that we can have fewer graphs and more > pairs? Weiwei, If you have the option of doing your own probe design, you can certainly exclude probes that have homology at any level you like. There are numerous papers on the subject of probe design and its limitations. If, by your question you mean, "Can the annotation of hgu133a be improved to have fewer graphs and more pairs?", is that really your highest priority? Sean