Problem with Expresso and RMA
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Monnie McGee ▴ 20
@monnie-mcgee-1106
Last seen 7.1 years ago
Dear BioC Users, I am analyzing data from an AffyBatch object (that I've called "allarray") with the following features: > print(allarray) AffyBatch object size of arrays=1164x1164 features (63515 kb) cdf=HG-U133_Plus_2 (54675 affyids) number of samples=6 number of genes=54675 annotation=hgu133plus2 Note that there are no replicates in this array. In other words, the 6 samples are 6 different arrays with 6 different RNA treatments. I'm trying to understand which genes are differentially expressed among the 6 arrays. I wanted to use RMA normalization, so I typed rma(allarray) and received the following error > eset1 <- rma(allarray) Background correcting Normalizing Calculating Expression Error in sigToEnv(signature, fdef) : Trying to get slot "signature" from an object of a basic class ("NULL") with no slots I tried to do the same thing using expresso and received the same error. Here's what I typed and the response of bioconductor: > eset1 <- expresso(allarray,bgcorrect.method="rma",normalize.method="quantiles", pm correct.method="pmonly",summary.method="medianpolish") background correction: rma normalization: quantiles PM/MM correction : pmonly expression values: mas background correcting...done. normalizing...Error in sigToEnv(signature, fdef) : Trying to get slot "signature" from an object of a basic class ("NULL") with no slots I read an archived message with said that it was not a good idea to use median polish without replicated arrays, and that it would be better to use rlm. However, I can't seem to get an eset so that I can use rlm. The funny thing is, just last week, expresso was working fine. I was able to obtain an eset with no errors, using the same AffyBatch with the same choices for all the methods. I would appreciate some help. Thanks, Monnie
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@vincent-j-carey-jr-4
Last seen 6 days ago
United States
To help you diagnose this we will need to know what version of R you are running, and what versions of affy and Biobase you have packageDescription("affy")$Version it would also be nice if you told us what platform you are using > Dear BioC Users, > > I am analyzing data from an AffyBatch object (that I've called > "allarray") with the following features: > > > print(allarray) > AffyBatch object > size of arrays=1164x1164 features (63515 kb) > cdf=HG-U133_Plus_2 (54675 affyids) > number of samples=6 > number of genes=54675 > annotation=hgu133plus2 > > Note that there are no replicates in this array. In other words, the 6 > samples are 6 different arrays with 6 different RNA treatments. I'm > trying to understand which genes are differentially expressed among the > 6 arrays. > > I wanted to use RMA normalization, so I typed rma(allarray) and > received the following error > > eset1 <- rma(allarray) > Background correcting > Normalizing > Calculating Expression > Error in sigToEnv(signature, fdef) : Trying to get slot "signature" > from an object of a basic class ("NULL") with no slots > > I tried to do the same thing using expresso and received the same > error. Here's what I typed and the response of bioconductor: > > eset1 > <- > expresso(allarray,bgcorrect.method="rma",normalize.method="quantiles ",pm > correct.method="pmonly",summary.method="medianpolish") > background correction: rma > normalization: quantiles > PM/MM correction : pmonly > expression values: mas > background correcting...done. > normalizing...Error in sigToEnv(signature, fdef) : Trying to get slot > "signature" from an object of a basic class ("NULL") with no slots > > I read an archived message with said that it was not a good idea to use > median polish without replicated arrays, and that it would be better to > use rlm. However, I can't seem to get an eset so that I can use rlm. > > The funny thing is, just last week, expresso was working fine. I was > able to obtain an eset with no errors, using the same AffyBatch with > the same choices for all the methods. > > I would appreciate some help. > > Thanks, > Monnie > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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McGee, Monnie ▴ 300
@mcgee-monnie-1108
Last seen 7.1 years ago
I am sorry. I know better than to leave out such important information. I am using R on a Macintosh Powerbook G4. I was using R through an X-windows interface (XFree86 4.3.0). The version of affy I am running is 1.5.8 and the Biobase version is 1.5.0. ________________________________ From: Vincent Carey 525-2265 [mailto:stvjc@channing.harvard.edu] Sent: Tue 2/15/2005 9:33 AM To: McGee, Monnie Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Problem with Expresso and RMA To help you diagnose this we will need to know what version of R you are running, and what versions of affy and Biobase you have packageDescription("affy")$Version it would also be nice if you told us what platform you are using > Dear BioC Users, > > I am analyzing data from an AffyBatch object (that I've called > "allarray") with the following features: > > > print(allarray) > AffyBatch object > size of arrays=1164x1164 features (63515 kb) > cdf=HG-U133_Plus_2 (54675 affyids) > number of samples=6 > number of genes=54675 > annotation=hgu133plus2 > > Note that there are no replicates in this array. In other words, the 6 > samples are 6 different arrays with 6 different RNA treatments. I'm > trying to understand which genes are differentially expressed among the > 6 arrays. > > I wanted to use RMA normalization, so I typed rma(allarray) and > received the following error > > eset1 <- rma(allarray) > Background correcting > Normalizing > Calculating Expression > Error in sigToEnv(signature, fdef) : Trying to get slot "signature" > from an object of a basic class ("NULL") with no slots > > I tried to do the same thing using expresso and received the same > error. Here's what I typed and the response of bioconductor: > > eset1 > <- > expresso(allarray,bgcorrect.method="rma",normalize.method="quantiles ",pm > correct.method="pmonly",summary.method="medianpolish") > background correction: rma > normalization: quantiles > PM/MM correction : pmonly > expression values: mas > background correcting...done. > normalizing...Error in sigToEnv(signature, fdef) : Trying to get slot > "signature" from an object of a basic class ("NULL") with no slots > > I read an archived message with said that it was not a good idea to use > median polish without replicated arrays, and that it would be better to > use rlm. However, I can't seem to get an eset so that I can use rlm. > > The funny thing is, just last week, expresso was working fine. I was > able to obtain an eset with no errors, using the same AffyBatch with > the same choices for all the methods. > > I would appreciate some help. > > Thanks, > Monnie > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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which R? it needs to be R 2.0.1 (or there abouts and not the 2.1.0 candidate) <more comments="" below=""> On Feb 15, 2005, at 10:14 AM, McGee, Monnie wrote: > I am sorry. I know better than to leave out such important > information. > > I am using R on a Macintosh Powerbook G4. I was using R through an > X-windows interface (XFree86 4.3.0). The version of affy I am running > is 1.5.8 and the Biobase version is 1.5.0. > > ________________________________ > > From: Vincent Carey 525-2265 [mailto:stvjc@channing.harvard.edu] > Sent: Tue 2/15/2005 9:33 AM > To: McGee, Monnie > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] Problem with Expresso and RMA > > > > To help you diagnose this we will need to know what version of R > you are running, and what versions of affy and Biobase you have > > packageDescription("affy")$Version > > it would also be nice if you told us what platform you are using > >> Dear BioC Users, >> >> I am analyzing data from an AffyBatch object (that I've called >> "allarray") with the following features: >> >>> print(allarray) >> AffyBatch object >> size of arrays=1164x1164 features (63515 kb) >> cdf=HG-U133_Plus_2 (54675 affyids) >> number of samples=6 >> number of genes=54675 >> annotation=hgu133plus2 >> >> Note that there are no replicates in this array. In other words, the >> 6 >> samples are 6 different arrays with 6 different RNA treatments. I'm >> trying to understand which genes are differentially expressed among >> the >> 6 arrays. >> >> I wanted to use RMA normalization, so I typed rma(allarray) and >> received the following error >>> eset1 <- rma(allarray) >> Background correcting >> Normalizing >> Calculating Expression >> Error in sigToEnv(signature, fdef) : Trying to get slot "signature" >> from an object of a basic class ("NULL") with no slots >> try traceback() right here something is confused about the class - where did you get the affyBatch object and are you sure it was created with the same version of affy as you are using >> I tried to do the same thing using expresso and received the same >> error. Here's what I typed and the response of bioconductor: >>> eset1 >> <- >> expresso(allarray,bgcorrect.method="rma",normalize.method="quantiles", >> pm >> correct.method="pmonly",summary.method="medianpolish") >> background correction: rma >> normalization: quantiles >> PM/MM correction : pmonly >> expression values: mas >> background correcting...done. >> normalizing...Error in sigToEnv(signature, fdef) : Trying to get slot >> "signature" from an object of a basic class ("NULL") with no slots >> >> I read an archived message with said that it was not a good idea to >> use >> median polish without replicated arrays, and that it would be better >> to >> use rlm. However, I can't seem to get an eset so that I can use rlm. >> >> The funny thing is, just last week, expresso was working fine. I was >> able to obtain an eset with no errors, using the same AffyBatch with >> the same choices for all the methods. >> >> I would appreciate some help. >> >> Thanks, >> Monnie >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > _______________________________________________ > 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 | +--------------------------------------------------------------------- -- ----------------+
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Linda Yue ▴ 10
@linda-yue-1113
Last seen 7.1 years ago
-----Original Message----- From: linda_yue@agilent.com To: bioconductor@stat.math.ethz.ch Cc: linda_fyue@emailservice.com; Xin.Liu@arradx.com Sent: Thu, 17 Feb 2005 08:35:50 -0700 Subject: Re: [BioC] Problem with Expresso and RMA Hi, What I use is the latest version of R: rw2001. And I got the following error message when I run RMA: Error in sigToEnv(signature, fdef) : Trying to get slot "signature" from an object of a basic class ("NULL") with no slots In addition: Warning message: Incompatible phenoData object. Created a new one. in: read.affybatch(filenames = files) Which information I should provide furthur or the latest version of R has some bugs? Thanks a lot! Xin LIU This e-mail is from ArraDx Ltd The e-mail and any files transmitted with it are confidentia...{{dropped}}
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@linda_yueagilentcom-1114
Last seen 7.1 years ago
Hi, What I use is the latest version of R: rw2001. And I got the following error message when I run RMA: Error in sigToEnv(signature, fdef) : Trying to get slot "signature" from an object of a basic class ("NULL") with no slots In addition: Warning message: Incompatible phenoData object. Created a new one. in: read.affybatch(filenames = files) Which information I should provide furthur or the latest version of R has some bugs? Thanks a lot! Xin LIU This e-mail is from ArraDx Ltd The e-mail and any files transmitted with it are confidentia...{{dropped}}
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