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Question: Could you help me
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gravatar for Liao, Guiping
12.8 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]]
ADD COMMENTlink modified 12.8 years ago by Holger Schwender900 • written 12.8 years ago by Liao, Guiping10
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gravatar for James W. MacDonald
12.8 years ago by
United States
James W. MacDonald45k 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
ADD COMMENTlink written 12.8 years ago by James W. MacDonald45k
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gravatar for Holger Schwender
12.8 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 +++ Superg√ľnstig und stressfrei einsteigen! AKTION "Kein Einrichtungspreis" nutzen: http://www.gmx.net/de/go/dsl
ADD COMMENTlink written 12.8 years ago by Holger Schwender900
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