User: Alex Sanchez

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Alex Sanchez90
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9 years, 8 months ago
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Posts by Alex Sanchez

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Answer: A: how to do it with biomaRt
... Hello Michal > The trick is that your IDs in the biomaRt filter are neither transcripts > nor compatible with "affy_raex_1_0_st_v1". It explains the empty return > Your IDs are Affy transcript clusters - a bit old way of defining features > on the Affy Exon chips, abandoned as > far ...
written 9.7 years ago by Alex Sanchez90
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how to do it with biomaRt
... Hello I am trying to use biomaRt for what seems to be a simple query. I have a list of transcript IDs from affymetrix Rat Exon arrays. I would like to get some associated identifiers such as the entrez gene id or th gene symbol. I have done the following ###################### library("biomaRt") ...
biomart written 9.7 years ago by Alex Sanchez90
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Answer: A: How to compare GO results
... Hello goProfiles works with 'organism' anotation packages ('org.XXX.XXX.db') There is an Arabidopsis annotation package 'org.At.tair.db' in the next version of BioC althoug I'm not sure if this is the one you need. You will find it in the Bioc-development site. http://www.bioconductor.org/packages/ ...
written 9.9 years ago by Alex Sanchez90
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Answer: A: How to compare GO results
... Hi Johannes There are several packages in BioC that you can use to do GO analysis or to mine GO analysis results. You can find most, if not all, of them in the Bioconductor GO task view. (Curiously topGO is not there). http://www.bioconductor.org/packages/release/GO.html I am the maintainer of th ...
written 9.9 years ago by Alex Sanchez90
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Answer: A: Changes in annotations?
... Hi James and thanks for the help. I know, of course, that what Bioconductor does is to take the annotations from public data sources. I will now turn to affymetrix to see if someone there, or in their forums, can explain why so many annotations have been turned into "NA's" There seem to be two pro ...
written 10.0 years ago by Alex Sanchez90
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Changes in annotations?
... Hello I have had to review recently an analysis I did some time ago. This was done on affymetrix hgu133plus2 chips with R 2.4 and BioC 1.9 I have re-run the analyses using R 2.9 and BioC 2.4 (sessionInfo below). I have been surprised by the changes in the annotations: Many probesets that had had an ...
annotation hgu133plus2 biobase annotate written 10.1 years ago by Alex Sanchez90
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Answer: A: error with ontoCompare (goTools)
... Hello Wolfgang I think you have found a bug which I skipped when moving from the old annotation system to the current .db based one. The problem seems to be simply that the internal affy-entrez conversion function is not working properly so you must convert it yourself before you call "basicProfile" ...
written 10.5 years ago by Alex Sanchez90
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Answer: A: error with ontoCompare (goTools)
... Hi WolfgangYou may want to try the 'goProfiles' package which is intended to do exactly what you're asking for, that is comparing two gene lists at a given level of the GO.I'd be happy to help if there appear any problems or to (try to) adapt any improvements you may suggest.BestAlex---------------- ...
written 10.5 years ago by Alex Sanchez90
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Combine hgu133a&b and hgu133plus2
... Hello I am re-analyzing two of studies that have been performed some time ago to compare good (GR) and bad (BR) responders to a treatment. The most recent study has been done using hgu133plus2. The other used a combination of hgu133plus and hgu133plus2 arrays. Specifically, two thirds of the arrays ...
normalization hgu133plus2 written 10.5 years ago by Alex Sanchez90 • updated 10.5 years ago by Charles Danko40

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