LocusLink query problem / bioC basic tutorial
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@huang-cheng-cheng-nihnci-192
Last seen 9.6 years ago
All: I have a LocusLink query problem when I run Dudoit's "Bioconductor basic tutorial". > library(annotate) > library(genefilter) > library(golubEsets) > library(ctest) > library(MASS) > library(mva) > library(cluster) > read.annotation("hgu6811") Error: couldn't find function "read.annotation" I am running R1.6.2 on Win2k, All latestest packages are used. According to the "help", it seems this function belongs to "annotate" package, which was loaded before the function called. Am I missing any packages or data files for this chip (hgu6811")? Thanks cc;
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@hinnerk-boriss-111
Last seen 9.6 years ago
Hi there, for teaching purposes I would like to cut down the number of genes in affybatch objects so that students won't have to wait that long for their computations. Unfortunately, I cannot figure out how to do that. Any hints? Thanks! Yours dreaming of good old plob objects, Hinnerk
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On Thu, May 22, 2003 at 03:06:15PM +0200, Hinnerk Boriss wrote: > Hi there, > > for teaching purposes I would like to cut down the number of genes in > affybatch objects so that students won't have to wait that long for > their computations. Unfortunately, I cannot figure out how to do that. > Any hints? Thanks! Cutting down the size of an AffyBatch is not straightforward (for the moment, it should be in the future). There are implications if one does so (think about the spatial background correction as done in mas 5.0). I believe that the "slowest" part is the computation of summary expression values. You may want to investigate the use of the parameter 'ids' for the method 'computeExprSet' (or 'summary.subset' for the function 'expresso', you can ask for the summary of a given set of affyids). > > Yours dreaming of good old plob objects, The release 1.0 of the package is still available for download I think... ;) Hopin' it helps, Laurent > Hinnerk > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
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Hinnek, i'd like to add there is a simple way to remove genes. its not the best way but its simple and itll do the trick: say ab is your affybatch and hgu95acdf is your cdf before your class type: 1) library(hgu95acdf) #probably already loaded 2) takeout <- ls(hgu95acdf)[1001:12626] 3) rm(list=takeout,envir=hgu95acdf) to get back to original hgu95acdf detach("package:hgu95acdf");library(hgu95acdf) AffyBatch's are not a simple as Plob's, but they make other things more efficient. On Thu, 22 May 2003, Laurent Gautier wrote: > On Thu, May 22, 2003 at 03:06:15PM +0200, Hinnerk Boriss wrote: > > Hi there, > > > > for teaching purposes I would like to cut down the number of genes in > > affybatch objects so that students won't have to wait that long for > > their computations. Unfortunately, I cannot figure out how to do that. > > Any hints? Thanks! > > Cutting down the size of an AffyBatch is not straightforward (for the > moment, it should be in the future). There are implications if one > does so (think about the spatial background correction as done > in mas 5.0). I believe that the "slowest" part is the computation of > summary expression values. You may want to investigate the use of the > parameter 'ids' for the method 'computeExprSet' > (or 'summary.subset' for the function 'expresso', > you can ask for the summary of a given set of affyids). > > > > > > > Yours dreaming of good old plob objects, > > The release 1.0 of the package is still available for download I think... > ;) > > > Hopin' it helps, > > > Laurent > > > > Hinnerk > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > -------------------------------------------------------------- > currently at the National Yang-Ming University in Taipei, Taiwan > -------------------------------------------------------------- > Laurent Gautier CBS, Building 208, DTU > PhD. Student DK-2800 Lyngby,Denmark > tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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> i'd like to add there is a simple way to remove genes. its > not the best > way but its simple and itll do the trick: > say ab is your affybatch and hgu95acdf is your cdf before > your class type: > > 1) library(hgu95acdf) #probably already loaded > 2) takeout <- ls(hgu95acdf)[1001:12626] > 3) rm(list=takeout,envir=hgu95acdf) > Rafael, I seem to be missing something. I've done the following: library(hgu95acdf) #probably already loaded takeout <- ls(hgu95acdf)[1001:12626] rm(list=takeout,envir=hgu95acdf) > junkab <- ReadAffy(widget=T) # reading in 4 hgu95av2 chips > junkab AffyBatch object size of arrays=640x640 features (12804 kb) cdf=HG_U95Av2 (12625 affyids) number of samples=4 number of genes=12625 annotation=hgu95av2 notes= Hmm, this still gives me all genes, even though the cdfenv has now only 1000 genes. Am I doing something wrong here? > AffyBatch's are not a simple as Plob's, but they make other things > more efficient. + I know, and I do appreciate those other aspects! > > > Yours dreaming of good old plob objects, > > > > The release 1.0 of the package is still available for > download I think... Laurent, will the release 1.0 be compatible with Wolfgang Huber's vsn package? I am afraid not. Best, Hinnerk
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you are using hgu95av2. so change it to the following: 1) data(hgu95av2cdf) #probably already loaded... 2) takeout <- ls(hgu95av2cdf)[1001:12626] 3) rm(list=takeout,envir=hgu95av2cdf) notice that hgu95av2cdf is included in the affy package (at least up to 1.1.2) so you dont need to load the library. Hinnerk Boriss wrote: > > > i'd like to add there is a simple way to remove genes. its > > not the best > > way but its simple and itll do the trick: > > say ab is your affybatch and hgu95acdf is your cdf before > > your class type: > > > > 1) library(hgu95acdf) #probably already loaded > > 2) takeout <- ls(hgu95acdf)[1001:12626] > > 3) rm(list=takeout,envir=hgu95acdf) > > > > Rafael, I seem to be missing something. I've done the following: > > library(hgu95acdf) #probably already loaded > takeout <- ls(hgu95acdf)[1001:12626] > rm(list=takeout,envir=hgu95acdf) > > junkab <- ReadAffy(widget=T) # reading in 4 hgu95av2 chips > > junkab > AffyBatch object > size of arrays=640x640 features (12804 kb) > cdf=HG_U95Av2 (12625 affyids) > number of samples=4 > number of genes=12625 > annotation=hgu95av2 > notes= > > Hmm, this still gives me all genes, even though the cdfenv has now only > 1000 genes. Am I doing something wrong here? > > > AffyBatch's are not a simple as Plob's, but they make other things > > more efficient. + > > I know, and I do appreciate those other aspects! > > > > > Yours dreaming of good old plob objects, > > > > > > The release 1.0 of the package is still available for > > download I think... > > Laurent, will the release 1.0 be compatible with Wolfgang Huber's vsn > package? I am afraid not. > > Best, > Hinnerk > >
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On Thu, May 22, 2003 at 05:07:46PM -0400, Rafael A. Irizarry wrote: > you are using hgu95av2. so change it to the following: > > 1) data(hgu95av2cdf) #probably already loaded... > 2) takeout <- ls(hgu95av2cdf)[1001:12626] > 3) rm(list=takeout,envir=hgu95av2cdf) > > notice that hgu95av2cdf is included in the affy package (at least up to > 1.1.2) so you dont need to load the library. I would like to stress that hgu95av2cdf *WAS* included in the package. It is now in a external package of example data (package 'affydata'). I would also like to comment on the approach you suggest. It is a nice idea, but can shoot in one's foot. The normalization methods work on "probes" (the slot 'exprs' in the AffyBatch). Some of these methods work with PMs, some with all the probes without considering the mapping (PM, MM or else). By modifying the associated cdfenv, one only modifies the mapping. Comparison of the processing methods of the data could be risky (and I would suspect that a teaching session would make students have a glance at that). The use of a subset of affyids suggested before is safe. Finally, to answer the qustion about VSN and affy 1.0. It won't work out of the box, but the mecanism for additional processing methods was already there. You could port vsn for Plobs. Hopin' it helps, L. > > Hinnerk Boriss wrote: > > > > > > i'd like to add there is a simple way to remove genes. its > > > not the best > > > way but its simple and itll do the trick: > > > say ab is your affybatch and hgu95acdf is your cdf before > > > your class type: > > > > > > 1) library(hgu95acdf) #probably already loaded > > > 2) takeout <- ls(hgu95acdf)[1001:12626] > > > 3) rm(list=takeout,envir=hgu95acdf) > > > > > > > Rafael, I seem to be missing something. I've done the following: > > > > library(hgu95acdf) #probably already loaded > > takeout <- ls(hgu95acdf)[1001:12626] > > rm(list=takeout,envir=hgu95acdf) > > > junkab <- ReadAffy(widget=T) # reading in 4 hgu95av2 chips > > > junkab > > AffyBatch object > > size of arrays=640x640 features (12804 kb) > > cdf=HG_U95Av2 (12625 affyids) > > number of samples=4 > > number of genes=12625 > > annotation=hgu95av2 > > notes= > > > > Hmm, this still gives me all genes, even though the cdfenv has now only > > 1000 genes. Am I doing something wrong here? > > > > > AffyBatch's are not a simple as Plob's, but they make other things > > > more efficient. + > > > > I know, and I do appreciate those other aspects! > > > > > > > Yours dreaming of good old plob objects, > > > > > > > > The release 1.0 of the package is still available for > > > download I think... > > > > Laurent, will the release 1.0 be compatible with Wolfgang Huber's vsn > > package? I am afraid not. > > > > Best, > > Hinnerk > > > > > -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
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as pointed out by laurent, this not something you want to do for serious analysis. hinnek asked for something to make examples in class go a little faster, for which i think this approach is totally ok. On Fri, 23 May 2003, Laurent Gautier wrote: > On Thu, May 22, 2003 at 05:07:46PM -0400, Rafael A. Irizarry wrote: > > you are using hgu95av2. so change it to the following: > > > > 1) data(hgu95av2cdf) #probably already loaded... > > 2) takeout <- ls(hgu95av2cdf)[1001:12626] > > 3) rm(list=takeout,envir=hgu95av2cdf) > > > > notice that hgu95av2cdf is included in the affy package (at least up to > > 1.1.2) so you dont need to load the library. > > I would like to stress that hgu95av2cdf *WAS* included in the package. > It is now in a external package of example data (package 'affydata'). > > I would also like to comment on the approach you suggest. It is a nice > idea, but can shoot in one's foot. The normalization methods work > on "probes" (the slot 'exprs' in the AffyBatch). Some of these methods > work with PMs, some with all the probes without considering the mapping > (PM, MM or else). By modifying the associated cdfenv, one only modifies > the mapping. Comparison of the processing methods of the data could be > risky (and I would suspect that a teaching session would make students > have a glance at that). The use of a subset of affyids suggested before > is safe. > > Finally, to answer the qustion about VSN and affy 1.0. It won't work out > of the box, but the mecanism for additional processing methods was already > there. You could port vsn for Plobs. > > > > Hopin' it helps, > > > > L. > > > > > > > > Hinnerk Boriss wrote: > > > > > > > > > i'd like to add there is a simple way to remove genes. its > > > > not the best > > > > way but its simple and itll do the trick: > > > > say ab is your affybatch and hgu95acdf is your cdf before > > > > your class type: > > > > > > > > 1) library(hgu95acdf) #probably already loaded > > > > 2) takeout <- ls(hgu95acdf)[1001:12626] > > > > 3) rm(list=takeout,envir=hgu95acdf) > > > > > > > > > > Rafael, I seem to be missing something. I've done the following: > > > > > > library(hgu95acdf) #probably already loaded > > > takeout <- ls(hgu95acdf)[1001:12626] > > > rm(list=takeout,envir=hgu95acdf) > > > > junkab <- ReadAffy(widget=T) # reading in 4 hgu95av2 chips > > > > junkab > > > AffyBatch object > > > size of arrays=640x640 features (12804 kb) > > > cdf=HG_U95Av2 (12625 affyids) > > > number of samples=4 > > > number of genes=12625 > > > annotation=hgu95av2 > > > notes= > > > > > > Hmm, this still gives me all genes, even though the cdfenv has now only > > > 1000 genes. Am I doing something wrong here? > > > > > > > AffyBatch's are not a simple as Plob's, but they make other things > > > > more efficient. + > > > > > > I know, and I do appreciate those other aspects! > > > > > > > > > Yours dreaming of good old plob objects, > > > > > > > > > > The release 1.0 of the package is still available for > > > > download I think... > > > > > > Laurent, will the release 1.0 be compatible with Wolfgang Huber's vsn > > > package? I am afraid not. > > > > > > Best, > > > Hinnerk > > > > > > > > > > -- > -------------------------------------------------------------- > currently at the National Yang-Ming University in Taipei, Taiwan > -------------------------------------------------------------- > Laurent Gautier CBS, Building 208, DTU > PhD. Student DK-2800 Lyngby,Denmark > tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent >
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> > for teaching purposes I would like to cut down the number > of genes in > > affybatch objects so that students won't have to wait that long for > > their computations. Unfortunately, I cannot figure out how > to do that. > > Any hints? Thanks! > > Cutting down the size of an AffyBatch is not straightforward (for the > moment, it should be in the future). There are implications if one > does so (think about the spatial background correction as done > in mas 5.0). I believe that the "slowest" part is the computation of > summary expression values. You may want to investigate the use of the > parameter 'ids' for the method 'computeExprSet' > (or 'summary.subset' for the function 'expresso', > you can ask for the summary of a given set of affyids). I've played with this, but it doesn't really help much because the student's computers are a bit on the slow end. How was the affybatch.example object created from the Lemon data? If its not too painful, I could try this approach. Best, Hinnerk
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 9.0 years ago
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Hi, You didn't say where you got the tutorial from -- some are very old (and I believe that this is one of those ones). read.annotation went away about a year ago.... If you are looking at somthing like this ################################################### ### chunk number 14: R ################################################### ll <- read.annotation("hgu68ll") # Read in locus link annotation data gname <- row.names(X2) # Names of genes with small p--value LocusID<-multiget(gname, env=ll) # Locus link IDs locuslinkByID(LocusID) # Query LocusLink Then, using the new system (and you probably want to use R 1.7.0 patched rather than 1.6.2). First obtain the hu6800 library library(hu6800) gname <- row.names(X2) LocusID<- getLL(gname, "hu6800") Robert On Thu, May 22, 2003 at 08:29:02AM -0400, Huang, Cheng-Cheng (NIH/NCI) wrote: > All: > > I have a LocusLink query problem when I run Dudoit's "Bioconductor basic > tutorial". > > library(annotate) > > library(genefilter) > > library(golubEsets) > > library(ctest) > > library(MASS) > > library(mva) > > library(cluster) > > read.annotation("hgu6811") > Error: couldn't find function "read.annotation" > > > I am running R1.6.2 on Win2k, All latestest packages are used. According to > the "help", it seems this function belongs to "annotate" package, which was > loaded before the function called. Am I missing any packages or data files > for this chip (hgu6811")? > > Thanks > > cc; > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+
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