suggestion : new object for exprSet

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Adaikalavan Ramasamy ★ 1.8k

@adaikalavan-ramasamy-675

Last seen 10.2 years ago

Would it be possible to have preprocessing algorithms in BioConductor (e.g RMA, GCRMA, MAS 5.0) to _automatically_ include a description of how the data was preprocessed into the resulting exprSet object ? It could say the algorithm name and BioConductor package version. For example typing in preproc( exprSet ) could return "Preprocessed using GCRMA version 1.1.3 and hgu133aprobe version 1.0" I am aware that I can manually add these info using notes() but am usually too lazy to do that. Then I spend hours trying to figure out what version of the GCRMA I used to create the dataset 3 months ago. Thank you. Regards, Adai

Preprocessing gcrma Preprocessing gcrma • 986 views

ADD COMMENT • link updated 19.7 years ago by Seth Falcon ★ 7.4k • written 19.7 years ago by Adaikalavan Ramasamy ★ 1.8k

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Seth Falcon ★ 7.4k

@seth-falcon-992

Last seen 10.2 years ago

Hi Adai, Adaikalavan Ramasamy <ramasamy@cancer.org.uk> writes: > Would it be possible to have preprocessing algorithms in BioConductor > (e.g RMA, GCRMA, MAS 5.0) to _automatically_ include a description of > how the data was preprocessed into the resulting exprSet object ? I like this idea and will suggest it to the team here. + seth

ADD COMMENT • link 19.7 years ago Seth Falcon ★ 7.4k

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On Mon, Mar 21, 2005 at 10:07:42AM -0800, Seth Falcon wrote: > Hi Adai, > > Adaikalavan Ramasamy <ramasamy@cancer.org.uk> writes: > > Would it be possible to have preprocessing algorithms in BioConductor > > (e.g RMA, GCRMA, MAS 5.0) to _automatically_ include a description of > > how the data was preprocessed into the resulting exprSet object ? > > I like this idea and will suggest it to the team here. I think it should be implemented by automatically adding some lines to the "notes" slot. exprSets are used for a lot of things and I do not think it is appropriate to have a "pre-process" slot which might not be relevant for all uses. Kasper

ADD REPLY • link 19.7 years ago Kasper Daniel Hansen ▴ 630

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I was not aware the exprSet was more generic that I am lead to believe. Would the information in 'notes' be overwritten by any genuine notes that the user makes ? This is the reason why I suggested a separate field but if it is easier to implement with 'notes', I am just as happy. Thank you. Regards, Adai On Mon, 2005-03-21 at 20:54 +0100, Kasper Daniel Hansen wrote: > On Mon, Mar 21, 2005 at 10:07:42AM -0800, Seth Falcon wrote: > > Hi Adai, > > > > Adaikalavan Ramasamy <ramasamy@cancer.org.uk> writes: > > > Would it be possible to have preprocessing algorithms in BioConductor > > > (e.g RMA, GCRMA, MAS 5.0) to _automatically_ include a description of > > > how the data was preprocessed into the resulting exprSet object ? > > > > I like this idea and will suggest it to the team here. > > I think it should be implemented by automatically adding some lines to > the "notes" slot. exprSets are used for a lot of things and I do not > think it is appropriate to have a "pre-process" slot which might not be > relevant for all uses. > > Kasper > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

ADD REPLY • link 19.7 years ago Adaikalavan Ramasamy ★ 1.8k

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