User: Lina Hultin-Rosenberg

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Posts by Lina Hultin-Rosenberg

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Comment: C: GSEABase error parsing msigdb_v3.1.xml
... Thanks a lot for the help and information! Best, Lina -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: den 31 januari 2013 14:35 To: Lina Hultin-Rosenberg Cc: bioconductor at r-project.org Subject: Re: [BioC] GSEABase error parsing msigdb_v3.1.xml On 01/31/2013 02 ...
written 6.2 years ago by Lina Hultin-Rosenberg80
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GSEABase error parsing msigdb_v3.1.xml
... Dear list, I am getting an error when trying to parse the latest msigdb version from Broad. I suspect the problem is due to that Broad added another category (c6). Will the new category be included in GSEABase? Is there a way to parse only categories c1-c5, or an alternative way to get all categori ...
go infrastructure hgu95av2 biobase annotate graph category annotationdbi biocgenerics written 6.2 years ago by Lina Hultin-Rosenberg80 • updated 6.2 years ago by Martin Morgan ♦♦ 23k
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Comment: C: GO terms not found in goTools and GO
... Thank you so much for the information! I did not now exactly how the different packages worked, now I know and understand better the problems I ran into. I use biomart ensembl for the GO queries. Best regards, Lina Seth Falcon skrev: > Wolfgang Huber writes: > >> Dear Lena, >> & ...
written 11.7 years ago by Lina Hultin-Rosenberg80
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GO terms not found in goTools and GO
... Dear list, I have retrieved GO terms for lists of human genes using biomaRt, and I am now using the packages goTools and GO to get further information about the terms. I discovered that one of the terms extracted with biomaRt, GO:0060070, does not exist in goTools and GO. Does anyone know what migh ...
go biobase annotate gotools biomart written 11.7 years ago by Lina Hultin-Rosenberg80 • updated 11.7 years ago by Seth Falcon7.4k
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Answer: A: from RefSeq to GO terms / gene symbol to geneID
... Dear Simon and Sean, sorry to get back to this issue so late but I have tried out various options to try to solve it. I parsed the files you mentioned but did not get many hits since many of my proteins does not have a Entrez gene id for some reason. In my search I also tried some of the Entrez e-u ...
written 11.7 years ago by Lina Hultin-Rosenberg80
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Answer: A: from RefSeq to GO terms / gene symbol to geneID
... Thank you so much for your help, I will try those alternatives out. Best, Lina Simon Lin skrev: > In the following two unrelated messages, both Sean and Nianhua suggested > to download and parse some data tables from the NCBI. The gene_info and > several other tables seems very useful. If ...
written 11.8 years ago by Lina Hultin-Rosenberg80
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from RefSeq GI protein identifiers to GO terms
... I just tried to send this mail to the list but it seems as if it didn't go through - I will make another try. ______________________________________________________________________ ___ Dear list, This might be a question that has been discussed previously but I could not find any good solution for ...
proteomics coverage go written 11.8 years ago by Lina Hultin-Rosenberg80
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Comment: C: Question about patchwork affy pre-processing
... Dear list, This might be a question that has been discussed previously but I could not find any good solution for it. I have lists of human proteins from various proteomics studies that I want to compare with regards to the GO terms associated to them. I have the RefSeq GI protein id for the protei ...
written 11.8 years ago by Lina Hultin-Rosenberg80

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