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Howard Schumacher ▴ 10

@howard-schumacher-1187

Last seen 10.2 years ago

Morning everyone. I don't know how many of you there are, so to those of you that have n opart in the following matter, I apologize for the intrusion. I'm supporting a user who would like to use Bioconductor R in a lab environment. Your site says "users are encouraged to use getBioC to obtain, install and update their packages". No thanks. It doesn't save bandwidth or shorten the download time. getBioC is also an impairment to using one's admin console, and eliminates any possibility of performing the installation off-line if needs be. I'd prefer a web link for "all" packages. There is no such web link though. The FAQ didn't explain why. The http://cran.r-project.org/bin/macosx/RAqua-FAQ.html page was not available. I'd appreciate the link in any form, published or unpublished. thanks a mil, h -- -------------------------------------------------------- Howard Schumacher Walkway Node, Support Manager State University of New York at Buffalo Amherst, New York 14260 United States Of America Earth http://www.buffalo.edu/~hss/ "Oooh! Ahhh! That's how it always starts, but then later there's running and then screaming." - Dr. Ian Malcolm

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ADD COMMENT • link updated 19.6 years ago by Jiuzhou song ▴ 100 • written 19.7 years ago by Howard Schumacher ▴ 10

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Adaikalavan Ramasamy ★ 1.8k

@adaikalavan-ramasamy-675

Last seen 10.2 years ago

1) Please use an informative subject line 2) Please search the appropriate FAQ and the mailing archives. The link that you provide (which does not exist) is for R not BioConductor. The correct documentation and section can be found at http://www.bioconductor.org/faq.html#downloading . Next, you can naively simply do a "wget" on the links given here recursively and extract the packages you need. 3) I feel this is a better option than above. On an interactive terminal, try the following : library(reposTools) z <- repositories() # now enter 2 for BioConductor Release 1.5 Source repository download.packages2( repEntry=z, destDir="/tmp" ) and hopefully they should be in the /tmp/ directory. On aside, I do not fully understand why the BioConductor core recommends on using getBioC.R script from the web instead of hard-coding it into R but I guess it is because the field is quite dynamic and they want the changes to be reflected immediately. Regards, Adai On Thu, 2005-04-07 at 11:16 -0400, Howard Schumacher wrote: > Morning everyone. > > I don't know how many of you there are, so to those of you that have > n opart in the following matter, I apologize for the intrusion. > > I'm supporting a user who would like to use Bioconductor R in a lab > environment. Your site says "users are encouraged to use getBioC to > obtain, install and update their packages". No thanks. It doesn't > save bandwidth or shorten the download time. getBioC is also an > impairment to using one's admin console, and eliminates any > possibility of performing the installation off-line if needs be. > > I'd prefer a web link for "all" packages. There is no such web link > though. The FAQ didn't explain why. The > http://cran.r-project.org/bin/macosx/RAqua-FAQ.html page was not > available. > > I'd appreciate the link in any form, published or unpublished. > > thanks a mil, > h > >

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

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Seth Falcon ★ 7.4k

@seth-falcon-992

Last seen 10.2 years ago

Hi Howard, Howard Schumacher <hss@buffalo.edu> writes: > I'm supporting a user who would like to use Bioconductor R in a lab > environment. Your site says "users are encouraged to use getBioC to > obtain, install and update their packages". No thanks. Next time, you might consider that a request for help will be more effective when you use a tone containing just a bit more politeness. > it doesn't save bandwidth or shorten the download time. Clearly, you have to download the Bioc packages once, but I understand the desire _not_ to download them for each system (as would happen with repeated calls to getBioC). > getBioC is also an impairment to using one's admin console, Eh? > I'd prefer a web link for "all" packages. There is no such web link > though. The FAQ didn't explain why. It isn't a FAQ! You can either use wget (yes, we could arrange are pages so this is easier, and it is something we will do in time). Or you can install the reposTools package and use download.packages2 along with the repositories function. Here's an untested R snippet: library(reposTools) rep = repositories() ## select what you want, probably 2 download.packages2(repEntry=rep, destdir=YOURDIRHERE) + seth

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

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Jiuzhou song ▴ 100

@jiuzhou-song-1051

Last seen 10.2 years ago

Hi, I want to creat a exprSet class, it combines expression data and phenotype data together. expression data is a matrix with columns representing patients and rows respresent genes. The phenoData contains the patient level, the column represent level and the rows represent patients. The format of the two datasets are shown below: The gene expression data: P01 P02 P03 P04 P05 P06 P07 P08 P09 P10 P11 P12 P13 P14 P15 1007_s_at 1336.97 1244.81 1242.41 1514.92 1531.80 1244.61 1030.43 967.83 866.32 1253.16 1218.51 1518.09 1401.07 1281.88 1438.96 ........ the phenotype data: Patient Phenotype P01 Def P02 Def P03 Def ...... My codes: >x<-read.table("exprstry.txt", header=TRUE) >y<-read.table("phenotype.txt", header=TRUE) >eset<-new('exprSet', exprs=x, phenoData=y) Error in validObject(.Object) : Invalid "exprSet" object: 1: Invalid object for slot "exprs" in class "exprSet": got class "data.frame", should be or extend class "exprMatrix" Invalid "exprSet" object: 2: Invalid object for slot "phenoData" in class "exprSet": got class "data.frame", should be or extend class "phenoData" Why it doesn't work. Thanks. Yours John

ADD COMMENT • link 19.6 years ago Jiuzhou song ▴ 100

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Hi John, Have you looked at the vignette in Biobase that explains how to do this? The short answer is that On Apr 16, 2005, at 7:52 AM, Jiuzhou song wrote: > Hi, > I want to creat a exprSet class, it combines expression data and > phenotype > data together. expression data is a matrix with columns representing > patients and rows respresent genes. The phenoData contains the patient > level, the column represent level and the rows represent patients. The > format of the two datasets are shown below: > > The gene expression data: > P01 P02 P03 P04 P05 P06 P07 P08 P09 P10 P11 P12 P13 P14 P15 > 1007_s_at 1336.97 1244.81 1242.41 1514.92 1531.80 1244.61 1030.43 > 967.83 866.32 > 1253.16 1218.51 1518.09 1401.07 1281.88 1438.96 > ........ > > the phenotype data: > > Patient Phenotype > P01 Def > P02 Def > P03 Def > ...... > > My codes: >> x<-read.table("exprstry.txt", header=TRUE) >> y<-read.table("phenotype.txt", header=TRUE) >> eset<-new('exprSet', exprs=x, phenoData=y) > Error in validObject(.Object) : Invalid "exprSet" object: 1: Invalid > object > for slot "exprs" in class "exprSet": got class "data.frame", should be > or > extend class "exprMatrix" read.table returns a data.frame, you need to turn that into a matrix (which is not the same thing) you might just want to check and see if the data is correct - has row names that are meaningful etc. the second argument needs to be an object of class phenoData, such objects do have a data.frame with the sample level covariate information but it also has a slot named varLabels where you should put a list which describes the variables in your data.frame (and hence these are self-documenting data structures). class?phenoData will give you information on the class. Robert An example copied straight from the vignette: library(Biobase) data(geneCov) data(geneData) covN <- list(cov1 = "Covariate 1; 2 levels", cov2 = "Covariate 2; 2 levels", cov3 = "Covariate 3; 3 levels") pD <- new("phenoData", pData=geneCov, varLabels=covN) eSet <- new("exprSet", exprs=geneData, phenoData=pD) > Invalid "exprSet" object: 2: Invalid object for slot "phenoData" in > class > "exprSet": got class "data.frame", should be or extend class > "phenoData" > > Why it doesn't work. > Thanks. > > Yours > > John > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+ +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+

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