Question: warning messages in gcrma
0
gravatar for Lizhe Xu
15.7 years ago by
Lizhe Xu210
Lizhe Xu210 wrote:
I just tried to run gcrma and got 30 warnings. I wonder if there are something I did wrong and if these warning affect my results. Thanks. > gcrmaDataB<-gcrma(DataB) Loading required package: hgu133bprobe Loading required package: matchprobes background correction: gcrma normalization: quantiles PM/MM correction : pmonly expression values: medianpolish background correcting...There were 30 warnings (use warnings() to see them) done. normalizing...done. 22645 ids to be processed ......... > warnings() Warning messages: 1: multi-argument returns are deprecated in: return(y = yhat, wt) 2: multi-argument returns are deprecated in: return(y = yhat, wt) 3: multi-argument returns are deprecated in: return(y = yhat, wt) 4: multi-argument returns are deprecated in: return(y = yhat, wt) 5: multi-argument returns are deprecated in: return(y = yhat, wt) 6: multi-argument returns are deprecated in: return(y = yhat, wt) 7: multi-argument returns are deprecated in: return(y = yhat, wt) 8: multi-argument returns are deprecated in: return(y = yhat, wt) 9: multi-argument returns are deprecated in: return(y = yhat, wt) 10: multi-argument returns are deprecated in: return(y = yhat, wt) 11: multi-argument returns are deprecated in: return(y = yhat, wt) 12: multi-argument returns are deprecated in: return(y = yhat, wt) 13: multi-argument returns are deprecated in: return(y = yhat, wt) 14: multi-argument returns are deprecated in: return(y = yhat, wt) 15: multi-argument returns are deprecated in: return(y = yhat, wt) 16: multi-argument returns are deprecated in: return(y = yhat, wt) 17: multi-argument returns are deprecated in: return(y = yhat, wt) 18: multi-argument returns are deprecated in: return(y = yhat, wt) 19: multi-argument returns are deprecated in: return(y = yhat, wt) 20: multi-argument returns are deprecated in: return(y = yhat, wt) 21: multi-argument returns are deprecated in: return(y = yhat, wt) 22: multi-argument returns are deprecated in: return(y = yhat, wt) 23: multi-argument returns are deprecated in: return(y = yhat, wt) 24: multi-argument returns are deprecated in: return(y = yhat, wt) 25: multi-argument returns are deprecated in: return(y = yhat, wt) 26: multi-argument returns are deprecated in: return(y = yhat, wt) 27: multi-argument returns are deprecated in: return(y = yhat, wt) 28: multi-argument returns are deprecated in: return(y = yhat, wt) 29: multi-argument returns are deprecated in: return(y = yhat, wt) 30: multi-argument returns are deprecated in: return(y = yhat, wt) Lizhe -----Original Message----- From: bioconductor-request@stat.math.ethz.ch [mailto:bioconductor- request@stat.math.ethz.ch] Sent: Monday, March 15, 2004 12:43 PM To: bioconductor@stat.math.ethz.ch Subject: Bioconductor Digest, Vol 13, Issue 30 Send Bioconductor mailing list submissions to bioconductor@stat.math.ethz.ch To subscribe or unsubscribe via the World Wide Web, visit https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor or, via email, send a message with subject or body 'help' to bioconductor-request@stat.math.ethz.ch You can reach the person managing the list at bioconductor-owner@stat.math.ethz.ch When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioconductor digest..." Today's Topics: 1. Re: questions about Affy package from new user: one more question (James MacDonald) 2. Re: MOE430 A and B (Ben Bolstad) 3. Re: utils required for EBarrays (A.J. Rossini) 4. Subsetting Affybatch objects by gene lists. (Horswell, Stuart) 5. Re: Minimum no. of chips for express/rma/gcrma etc (James MacDonald) 6. Re: SAM : warning messages problem (James MacDonald) 7. Re: Quantile normalization vs. data distributions (Naomi Altman) 8. question on making affy environment (Straubhaar, Juerg) 9. RE: questions about Affy package from new user: onemore question (Adaikalavan Ramasamy) ---------------------------------------------------------------------- Message: 1 Date: Mon, 15 Mar 2004 09:11:29 -0500 From: "James MacDonald" <jmacdon@med.umich.edu> Subject: Re: [BioC] questions about Affy package from new user: one more question To: <lxu@chnola-research.org>, <bioconductor@stat.math.ethz.ch> Message-ID: <s055735d.015@med-gwia-02a.med.umich.edu> Content-Type: text/plain; charset=US-ASCII AH. GS==GeneSpring. If you want to join them before importing to GeneSpring, you should do this after computing expression values. You can do something like: out <- rbind(exprs(exprSetA), exprs(exprSetB)) write.table(out, "Combined expression data.txt", sep="\t", quote=F, col.names=NA) HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Lizhe Xu" <lxu@chnola-research.org> 03/14/04 06:20PM >>> Now, I tried to load the exported data from Bioconductor to GeneSpring and found another question. Since I used U133 chip set, I wonder if I can joint the U133A and B directly and import them to GS or I should do probeset level normalization first (if so, which package in bioconductor can do it) before joint them. Thanks. Lxu _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ------------------------------ Message: 2 Date: Mon, 15 Mar 2004 06:17:23 -0800 From: Ben Bolstad <bolstad@stat.berkeley.edu> Subject: Re: [BioC] MOE430 A and B To: peter robinson <peter.robinson@t-online.de> Cc: bioconductor@stat.math.ethz.ch Message-ID: <1079360243.1562.2.camel@bmbbox.dyndns.org> Content-Type: text/plain you need to read in the type A and type B files into separate affybatch objects. eg my.Data.A <- ReadAffy(filenames=c("blahA1.cel","blahA2.cel","blahA3.cel")) my.Data.B <- ReadAffy(filenames=c("blahB1.cel","blahB2.cel","blahB3.cel")) Ben On Mon, 2004-03-15 at 04:20, peter robinson wrote: > Dear List members, > > I would like to use the affy package to analyze data from MOE430A and -B > chips. I tried to read in data from both types of chips at once using > data <- ReadAffy(widget=T) > and then reading in 3 MOE430A and 3 MOE430B CEL files. > I got the error message: > "Cel file does not seem to beo of 430MOEA type" when the script tried to input > data from a 430MOEB Cel file. I had imported the CDF and annotation packages > for both types of chip. > I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system. > > Thanks for any advice/tips! > > Peter > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad ------------------------------ Message: 3 Date: Mon, 15 Mar 2004 06:22:12 -0800 From: rossini@blindglobe.net (A.J. Rossini) Subject: Re: [BioC] utils required for EBarrays To: <arne.muller@aventis.com> Cc: bioconductor@stat.math.ethz.ch Message-ID: <85wu5mb36z.fsf@servant.blindglobe.net> Content-Type: text/plain; charset=us-ascii As I tried to write clearly in my last email about the upcoming release, you MUST use the Devel branch of R with packages in the devel branch of Bioconductor. best, -tony <arne.muller@aventis.com> writes: > Hello, > > I'm running BioC 1.3 and R 1.8.1. I've tried to install the EBarrays > pacckage from the devel branch, but get the following error: > >> install.packages2('EBarrays', force=T) > Note: You did not specify a download type. Using a default value of: Source > This will be fine for almost all users > > [1] "Attempting to download EBarrays from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing EBarrays" > * Installing *source* package 'EBarrays' ... > ** libs > gcc -I/tgx/soft/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES > -mieee-fp -fPIC -g -O2 -c ebarrays.c -o ebarrays.o > gcc -shared -L/usr/local/lib -o EBarrays.so ebarrays.o > -L/tgx/soft/lib/R/bin -lR > ** R > ** data > ** demo > ** inst > ** save image > Error: Requires utils to run properly > In addition: Warning message: > There is no package called 'utils' in: library(package, character.only = > TRUE, logical = TRUE, warn.conflicts = warn.conflicts, > Execution halted > /tgx/soft/lib/R/bin/INSTALL: line -116: 2881 Broken pipe cat > "/tgx/soft/lib/R/library/EBarrays/R/EBarrays" > ERROR: execution of package source for 'EBarrays' failed > ** Removing '/tgx/soft/lib/R/library/EBarrays' > Warning message: > Installation of package EBarrays had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >>From URL: http://www.bioconductor.org/repository/devel/package/Source > EBarrays version 1.0-17 > > I cannot find the utils package, where is it locatd in the BioC repositories? > Can I install EBarrays without installing the complete develompent branch? > > kind regards + thank for your help, > > Arne > > -- > Arne Muller, Ph.D. > Toxicogenomics, Aventis Pharma > arne dot muller domain=aventis com > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}} ------------------------------ Message: 4 Date: Mon, 15 Mar 2004 14:22:03 -0000 From: "Horswell, Stuart" <stuart.horswell@csc.mrc.ac.uk> Subject: [BioC] Subsetting Affybatch objects by gene lists. To: <bioconductor@stat.math.ethz.ch> Message-ID: <a09f613372b70c4cbce35a9095f434f009ffe9@icex34.cc.ic.ac.uk> Content-Type: text/plain; charset="iso-8859-1" Hi all, I'm trying to run an analysis on 24 Affymetrix HGu95v2 chips. I've set up, via merge.AffyBatch, an affybatch object containing all 24 arrays. A1 <- read.affybatch("A1.cel") . . . A24 <- read.affybatch("A24.cel") A <- merge.AffyBatch(A1, A2) A <- merge.AffyBatch(A, A3) . . . A<- merge.AffyBatch(A, A24) I then computed MAS5 type Present/Absent calls for each array using mas5calls. A.calls <- mas5calls(A) p.a.A <- exprs(A.calls) What I'd like to do now is remove all of those genes without a single present call across all 24 arrays before normalizing. I can use the p.a.A file to obtain a list of the gene names/affy id tags that I want to remove but I can't figure out how to delete the relavent probe pairs from my affybatch object. In fact that only things I've been able to find on the mailing list archive and/or vignettes are how to subset by array or how to remove chunks from the cdf environment - but this presents me with two problems, first I'm not sure I can get the pattern matching working well enough to identify which entry numbers in the cdf file correspond to the gene list I have, and secondly, people have already commented that this isn't neccessarily a sensible approach for proper analysis anyway. So I'm kind of stumped now! Any help or advice would be most greatfully received, many thanks, Stu ------------------------------ Message: 5 Date: Mon, 15 Mar 2004 09:24:44 -0500 From: "James MacDonald" <jmacdon@med.umich.edu> Subject: Re: [BioC] Minimum no. of chips for express/rma/gcrma etc To: <bioconductor@stat.math.ethz.ch>, <aedin.culhane@ucd.ie> Message-ID: <s055766d.081@med-gwia-02a.med.umich.edu> Content-Type: text/plain; charset=US-ASCII I think you can argue that the batch methods (rma, gcrma) require more than a certain number of chips to accurately estimate the parameters you are modeling. However, this probably only applies to genes that are not changing that much, so you will still see the ones that really change. I don't think mas5 is affected by the number of chips. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Aedin <aedin.culhane@ucd.ie> 03/15/04 07:20AM >>> Dear BioC Are rma/gcrma/mas5.0/ etc limited by a minimum number of chip (.cel) files? I am calling expression values on a dataset with only 2 chips (treated/control, pooled RNA from n=5). Is 2 chips too few .cel files for these methods? Thanks for your help Aedin _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ------------------------------ Message: 6 Date: Mon, 15 Mar 2004 09:27:49 -0500 From: "James MacDonald" <jmacdon@med.umich.edu> Subject: Re: [BioC] SAM : warning messages problem To: <willy.wynant@curie.fr>, <bioconductor@stat.math.ethz.ch> Message-ID: <s0557732.029@med-gwia-02a.med.umich.edu> Content-Type: text/plain; charset=US-ASCII This is really only a problem for the package maintainer. Your results are not affected. Basically there has been a change in R, and siggenes has not been modified to account for that change. Right now everything is still working correctly, you just have a bunch of annoying error messages. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Willy Wynant <willy.wynant@curie.fr> 03/15/04 07:57AM >>> Hi, I am using siggenes package and I am encountering problems with warning messages with the function sam. For example, if I type : res<-sam(data,3:11,12:88,B=1000,alpha.s0=seq(0,1,0.02),factor.s0=1.482 6,delta.fdr=(1:10)/10,rand=123,vec.lambda.p0=(0:95)/100,ngenes=NA,iter ation=10,initial.delta=(1:20)/10) I've got as result the SAM analysis and the following answer: Warning messages : 1:multi-argument returns are deprecated in : return(r,s,r.perm,s.perm,Z,mat.samp,var.0.genes,NA.genes) 2:multi-argument returns are deprecated in : return(alpha.hat,s.zero,cv,cv.zero) 3:multi-argument returns are deprecated in : return(p0,spline.out,vec.p0) 4:multi-argument returns are deprecated in : return(tab.fdr,mat.fdr,p0) 5 :multi-argument returns are deprecated in : return(d,d.sort,s,d.bar,d.perm,mat.samp,s0,FDR,p0,fdr.ngenes, I installed the R.1.8.1 version. Could you help me ? Thank you _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ------------------------------ Message: 7 Date: Mon, 15 Mar 2004 10:04:57 -0500 From: Naomi Altman <naomi@stat.psu.edu> Subject: Re: [BioC] Quantile normalization vs. data distributions To: "Stan Smiley" <swsmiley@genetics.utah.edu>, "Bioconductor Mailing list" <bioconductor@stat.math.ethz.ch> Message-ID: <6.0.0.22.2.20040314225049.01d7ffb8@stat.psu.edu> Content-Type: text/plain; charset="us-ascii"; format=flowed This is a very good question that I have also been puzzling over. It seems useless to try tests of equality of the distribution such as Kolmogorov-Smirnov- due to the huge sample size you would almost certainly get a significant result. Currently, I am using the following graphical method: 1. I compute a kernel density estimate of the combined data of all probes on all the arrays. 2. I compute a kernel density estimate of the data for each array. 3. I plot both smooths on the same plot, and decide if they are the same. Looking at what I wrote above, I think it would be better in steps 1 and 2 to background correct and center each array before combining. It might also be between to reduce the data to standardized scores before combining, unless you think that the overall scaling is due to your "treatment effect". It seems like half of what I do is ad hoc, so I always welcome any criticisms or suggestions. --Naomi Altman At 06:07 PM 3/11/2004, Stan Smiley wrote: >Greetings, > >I have been trying to find a quantitative measure to tell when the data >distributions >between chips are 'seriously' different enough from each other to violate >the >assumptions behind quantile normalization. I've been through the archives >and seen some discussion of this matter, but didn't come away with a >quantitative measure I >could apply to my data sets to assure me that it would be OK to use quantile >normalization. > > >"Quantile normalization uses a single standard for all chips, however it >assumes that no serious change in distribution occurs" > >Could someone please point me in the right direction on this? > >Thanks. > >Stan Smiley >stan.smiley@genetics.utah.edu > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111 ------------------------------ Message: 8 Date: Mon, 15 Mar 2004 10:33:00 -0500 From: "Straubhaar, Juerg" <juerg.straubhaar@umassmed.edu> Subject: [BioC] question on making affy environment To: <bioconductor@stat.math.ethz.ch> Message-ID: <1A42F1E1A1E73A4F8C6048789F34A32F2D8AF5@edunivmail02.ad.umassmed.edu> Content-Type: text/plain; charset="Windows-1252" I would like to make a mixed environment for the mouse U74B (and C separately) version 1 and 2 chip set using common probesets. I know Ben Bolstad has built such a mixted environment for the U74 A chip. How do you do this? There are 5 library files for each chip. Do I have to create new library files containing only the common probesets and then using the make.cdf.package? I would be grateful for suggestions on how to proceed. Juerg Straubhaar Umass Med School ------------------------------ Message: 9 Date: Mon, 15 Mar 2004 16:22:42 -0000 From: "Adaikalavan Ramasamy" <ramasamy@cancer.org.uk> Subject: RE: [BioC] questions about Affy package from new user: onemore question To: "James MacDonald" <jmacdon@med.umich.edu>, <lxu@chnola-research.org>, <bioconductor@stat.math.ethz.ch> Message-ID: <odepicohndbjehifcimpkeekcbaa.ramasamy@cancer.org.uk> Content-Type: text/plain; charset="US-ASCII" The rownames of HGU-133A and HGU-133B are not unique (there is about 100+ redundancies). You might want to add these codes before rbind() to avoid any confusion later. A <- exprs(exprSetA) rownames(A) <- paste("A.", rownames(A)) B <- exprs(exprSetB) rownames(B) <- paste("B.", rownames(B)) Also, doing normalization before summary is better because we have more information to utilize at probe level. > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of James > MacDonald > Sent: 15 March 2004 14:11 > To: lxu@chnola-research.org; bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] questions about Affy package from new user: onemore > question > > > AH. GS==GeneSpring. > > If you want to join them before importing to GeneSpring, you should do > this after computing expression values. You can do something like: > > out <- rbind(exprs(exprSetA), exprs(exprSetB)) > write.table(out, "Combined expression data.txt", sep="\t", quote=F, > col.names=NA) > > HTH, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> "Lizhe Xu" <lxu@chnola-research.org> 03/14/04 06:20PM >>> > Now, I tried to load the exported data from Bioconductor to GeneSpring > and found another question. Since I used U133 chip set, I wonder if I > can joint the U133A and B directly and import them to GS or I should do > probeset level normalization first (if so, which package in bioconductor > can do it) before joint them. Thanks. > > Lxu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor End of Bioconductor Digest, Vol 13, Issue 30
ADD COMMENTlink modified 15.7 years ago by James W. MacDonald51k • written 15.7 years ago by Lizhe Xu210
Answer: warning messages in gcrma
0
gravatar for paolo.sirabella@uniroma1.it
15.7 years ago by
I got the same kind of warnings referred in the attached post by Lizhe Xu. The configuration is R1.8.1/BioC1.3/Linux . I have no idea of the meaning of these warnings and if they are significant. Does anyone give us some hints ? Thanks ---------------------------------------------------------------- Paolo Sirabella, PhD University of Rome - "La Sapienza" Dept. of Human Physiology and Pharmacology - Building of Human Physiology P.le Aldo Moro, 5 - 00185 Roma - Italy Web http://w3.uniroma1.it/cisb/Cisb/members/sirabella Simplex Sigillum Veri ---------------------------------------------------------------------- -- On 15 Mar 2004 at 15:22, Lizhe Xu wrote: > I just tried to run gcrma and got 30 warnings. I wonder if there are something I did wrong and if these warning affect my results. Thanks. > > > gcrmaDataB<-gcrma(DataB) > Loading required package: hgu133bprobe > Loading required package: matchprobes > background correction: gcrma > normalization: quantiles > PM/MM correction : pmonly > expression values: medianpolish > background correcting...There were 30 warnings (use warnings() to see them) > done. > normalizing...done. > 22645 ids to be processed > ......... > > warnings() > Warning messages: > 1: multi-argument returns are deprecated in: return(y = yhat, wt) > 2: multi-argument returns are deprecated in: return(y = yhat, wt) > 3: multi-argument returns are deprecated in: return(y = yhat, wt) > 4: multi-argument returns are deprecated in: return(y = yhat, wt) > 5: multi-argument returns are deprecated in: return(y = yhat, wt) > 6: multi-argument returns are deprecated in: return(y = yhat, wt) > 7: multi-argument returns are deprecated in: return(y = yhat, wt) > 8: multi-argument returns are deprecated in: return(y = yhat, wt) > 9: multi-argument returns are deprecated in: return(y = yhat, wt) > 10: multi-argument returns are deprecated in: return(y = yhat, wt) > 11: multi-argument returns are deprecated in: return(y = yhat, wt) > 12: multi-argument returns are deprecated in: return(y = yhat, wt) > 13: multi-argument returns are deprecated in: return(y = yhat, wt) > 14: multi-argument returns are deprecated in: return(y = yhat, wt) > 15: multi-argument returns are deprecated in: return(y = yhat, wt) > 16: multi-argument returns are deprecated in: return(y = yhat, wt) > 17: multi-argument returns are deprecated in: return(y = yhat, wt) > 18: multi-argument returns are deprecated in: return(y = yhat, wt) > 19: multi-argument returns are deprecated in: return(y = yhat, wt) > 20: multi-argument returns are deprecated in: return(y = yhat, wt) > 21: multi-argument returns are deprecated in: return(y = yhat, wt) > 22: multi-argument returns are deprecated in: return(y = yhat, wt) > 23: multi-argument returns are deprecated in: return(y = yhat, wt) > 24: multi-argument returns are deprecated in: return(y = yhat, wt) > 25: multi-argument returns are deprecated in: return(y = yhat, wt) > 26: multi-argument returns are deprecated in: return(y = yhat, wt) > 27: multi-argument returns are deprecated in: return(y = yhat, wt) > 28: multi-argument returns are deprecated in: return(y = yhat, wt) > 29: multi-argument returns are deprecated in: return(y = yhat, wt) > 30: multi-argument returns are deprecated in: return(y = yhat, wt) > > Lizhe
ADD COMMENTlink written 15.7 years ago by paolo.sirabella@uniroma1.it10
Answer: warning messages in gcrma
0
gravatar for James W. MacDonald
15.7 years ago by
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James W. MacDonald51k wrote:
These warnings are due to some changes that are occuring in R. They don't have any effect on your results, and they will go away with the new release of BioC. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> <paolo.sirabella@uniroma1.it> 03/16/04 8:28 AM >>> I got the same kind of warnings referred in the attached post by Lizhe Xu. The configuration is R1.8.1/BioC1.3/Linux . I have no idea of the meaning of these warnings and if they are significant. Does anyone give us some hints ? Thanks ---------------------------------------------------------------- Paolo Sirabella, PhD University of Rome - "La Sapienza" Dept. of Human Physiology and Pharmacology - Building of Human Physiology P.le Aldo Moro, 5 - 00185 Roma - Italy Web http://w3.uniroma1.it/cisb/Cisb/members/sirabella Simplex Sigillum Veri ---------------------------------------------------------------------- -- On 15 Mar 2004 at 15:22, Lizhe Xu wrote: > I just tried to run gcrma and got 30 warnings. I wonder if there are something I did wrong and if these warning affect my results. Thanks. > > > gcrmaDataB<-gcrma(DataB) > Loading required package: hgu133bprobe > Loading required package: matchprobes > background correction: gcrma > normalization: quantiles > PM/MM correction : pmonly > expression values: medianpolish > background correcting...There were 30 warnings (use warnings() to see them) > done. > normalizing...done. > 22645 ids to be processed > ......... > > warnings() > Warning messages: > 1: multi-argument returns are deprecated in: return(y = yhat, wt) > 2: multi-argument returns are deprecated in: return(y = yhat, wt) > 3: multi-argument returns are deprecated in: return(y = yhat, wt) > 4: multi-argument returns are deprecated in: return(y = yhat, wt) > 5: multi-argument returns are deprecated in: return(y = yhat, wt) > 6: multi-argument returns are deprecated in: return(y = yhat, wt) > 7: multi-argument returns are deprecated in: return(y = yhat, wt) > 8: multi-argument returns are deprecated in: return(y = yhat, wt) > 9: multi-argument returns are deprecated in: return(y = yhat, wt) > 10: multi-argument returns are deprecated in: return(y = yhat, wt) > 11: multi-argument returns are deprecated in: return(y = yhat, wt) > 12: multi-argument returns are deprecated in: return(y = yhat, wt) > 13: multi-argument returns are deprecated in: return(y = yhat, wt) > 14: multi-argument returns are deprecated in: return(y = yhat, wt) > 15: multi-argument returns are deprecated in: return(y = yhat, wt) > 16: multi-argument returns are deprecated in: return(y = yhat, wt) > 17: multi-argument returns are deprecated in: return(y = yhat, wt) > 18: multi-argument returns are deprecated in: return(y = yhat, wt) > 19: multi-argument returns are deprecated in: return(y = yhat, wt) > 20: multi-argument returns are deprecated in: return(y = yhat, wt) > 21: multi-argument returns are deprecated in: return(y = yhat, wt) > 22: multi-argument returns are deprecated in: return(y = yhat, wt) > 23: multi-argument returns are deprecated in: return(y = yhat, wt) > 24: multi-argument returns are deprecated in: return(y = yhat, wt) > 25: multi-argument returns are deprecated in: return(y = yhat, wt) > 26: multi-argument returns are deprecated in: return(y = yhat, wt) > 27: multi-argument returns are deprecated in: return(y = yhat, wt) > 28: multi-argument returns are deprecated in: return(y = yhat, wt) > 29: multi-argument returns are deprecated in: return(y = yhat, wt) > 30: multi-argument returns are deprecated in: return(y = yhat, wt) > > Lizhe _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 15.7 years ago by James W. MacDonald51k
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