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Question: Could you help me
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13.4 years ago by
Liao, Guiping10 wrote:
Dear everyone: I am employing the Bioconductor Packages such as Siggenes to analyse Microarray Data. My experiment is the two class paired case, according to arguments of siggenes, I set the cl as follows: > npr4.cl V1 V2 1 1 2 2 -1 2 3 1 5 4 -1 5 5 1 1 6 -1 1 7 1 3 8 -1 3 9 1 4 10 -1 4 I run the find.a0, it gives me a wrong message:unpaired case??? :: a0 <- find.a0(npr4,npr4.cl,B=26282,balanced=FALSE,mat.samp=NULL,delta=0.485, + alpha=(0:9)/10, include.0=TRUE,p0=NA,plot.legend=TRUE,na.rm=FALSE,rand=1234567) EBAM Analysis for the two class unpaired case. Warning: Expected classlabels are 0 and 1. cl will thus be set to 0 and 1. Error in "[<-.data.frame"(*tmp*, which(cl == min(lev)), value = 0) : new columns would leave holes after existing columns So, I dont know what's wrong? Yet that cl will be set to 0 and 1is for the unpaired case. I am sure that you can help me. Tthanks so much. Guiping Liao PBI, NRC, Canada [[alternative HTML version deleted]]
modified 13.4 years ago by Holger Schwender900 • written 13.4 years ago by Liao, Guiping10
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13.4 years ago by
United States
James W. MacDonald46k wrote:
Liao, Guiping wrote: > Dear everyone: > > I am employing the Bioconductor Packages such as Siggenes to analyse > Microarray Data. My experiment is the two class paired case, according to > arguments of siggenes, I set the cl as follows: > >>npr4.cl > > V1 V2 > 1 1 2 > 2 -1 2 > 3 1 5 > 4 -1 5 > 5 1 1 > 6 -1 1 > 7 1 3 > 8 -1 3 > 9 1 4 > 10 -1 4 From the help page for find.a0: cl: a vector containing the class labels of the samples. In the two class unpaired case, the label of a sample is either 0 (e.g., control group) or 1 (e.g., case group). In the two class paired case, the labels are the integers between 1 and n/2 (e.g., after treatment group) and between -1 and -n/2 (e.g., before treatment group), where n is the length of 'cl' and k is paired with -k. For one group data, the label for each sample should be 1. So find.a0 is expecting a vector rather than the matrix you are using. I believe you want something like: npr4.cl <- npr4.cl[,1]*npr4.cl[,2] You also don't have enough samples to do 26282 permutations, nor (I suspect) do you really want to wait that long. I would suggest something more reasonable like 500 or 1000. Jim > > I run the find.a0, it gives me a wrong message:unpaired case??? :: > > a0 <- > find.a0(npr4,npr4.cl,B=26282,balanced=FALSE,mat.samp=NULL,delta=0.485, > + alpha=(0:9)/10, > include.0=TRUE,p0=NA,plot.legend=TRUE,na.rm=FALSE,rand=1234567) > EBAM Analysis for the two class unpaired case. > > Warning: Expected classlabels are 0 and 1. cl will thus be set to 0 and 1. > > Error in "[<-.data.frame"(*tmp*, which(cl == min(lev)), value = 0) : > new columns would leave holes after existing columns > > So, I dont know what's wrong? Yet that cl will be set to 0 and 1is for the > unpaired case. > > I am sure that you can help me. > > Tthanks so much. > > Guiping Liao > PBI, NRC, Canada > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
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13.4 years ago by
Holger Schwender900 wrote:
The problem is that the specification of cl currently differs between SAM and EBAM. When performing a SAM analysis you can specify cl in the way that you have specified it. In an EBAM analysis, this way of specification is currently not implemented. I hope that I can implement this soon. This should be available latest in the next Bioconductor release. > Liao, Guiping wrote: > > Dear everyone: > > > > I am employing the Bioconductor Packages such as Siggenes to analyse > > Microarray Data. My experiment is the two class paired case, according > to > > arguments of siggenes, I set the cl as follows: > > > >>npr4.cl > > > > V1 V2 > > 1 1 2 > > 2 -1 2 > > 3 1 5 > > 4 -1 5 > > 5 1 1 > > 6 -1 1 > > 7 1 3 > > 8 -1 3 > > 9 1 4 > > 10 -1 4 > > From the help page for find.a0: > > cl: a vector containing the class labels of the samples. In the > two class unpaired case, the label of a sample is either 0 > (e.g., control group) or 1 (e.g., case group). In the two > class paired case, the labels are the integers between 1 and > n/2 (e.g., after treatment group) and between -1 and -n/2 > (e.g., before treatment group), where n is the length of 'cl' > and k is paired with -k. For one group data, the label for > each sample should be 1. > > So find.a0 is expecting a vector rather than the matrix you are using. I > believe you want something like: > > npr4.cl <- npr4.cl[,1]*npr4.cl[,2] > > You also don't have enough samples to do 26282 permutations, nor (I > suspect) do you really want to wait that long. I would suggest something > more reasonable like 500 or 1000. > > Jim > > > > > > I run the find.a0, it gives me a wrong message:unpaired case??? :: > > > > a0 <- > > find.a0(npr4,npr4.cl,B=26282,balanced=FALSE,mat.samp=NULL,delta=0.485, > > + alpha=(0:9)/10, > > include.0=TRUE,p0=NA,plot.legend=TRUE,na.rm=FALSE,rand=1234567) > > EBAM Analysis for the two class unpaired case. > > > > Warning: Expected classlabels are 0 and 1. cl will thus be set to 0 and > 1. > > > > Error in "[<-.data.frame"(*tmp*, which(cl == min(lev)), value = 0) : > > new columns would leave holes after existing columns > > > > So, I dont know what's wrong? Yet that cl will be set to 0 and 1is for > the > > unpaired case. > > > > I am sure that you can help me. > > > > Tthanks so much. > > > > Guiping Liao > > PBI, NRC, Canada > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- DSL Komplett von GMX +++ Supergünstig und stressfrei einsteigen! AKTION "Kein Einrichtungspreis" nutzen: http://www.gmx.net/de/go/dsl