Dear all, I have a data set consisted of 4 cell types with each cell type having 3 replicates. I find the unique signature genes of each cell types using decideTests (see following). I only want the top, say 20 signature probes that satisfy my thresholds. I tried to use "number=20" as for the "topTable" function with "decideTests", but it gave me the an error (see below). Is there a way that I can define the number of upregulated probes for outputting in decideTests? Thank you in advance, Wendy Code: results <- decideTests(fit[,-1], p=0.10, lfc=log2(2),number=20) Error in decideTests(fit[, -1], p = pval, lfc = log2(foldchange), number = 20) : unused argument(s) (number = 20) [[alternative HTML version deleted]]

On 06/09/2011 08:20 PM, Wendy Qiao wrote: > Dear all, > > I have a data set consisted of 4 cell types with each cell type having 3 > replicates. I find the unique signature genes of each cell types using > decideTests (see following). I only want the top, say 20 signature probes > that satisfy my thresholds. I tried to use "number=20" as for the > "topTable" function with "decideTests", but it gave me the an error (see > below). Is there a way that I can define the number of upregulated probes > for outputting in decideTests? Hi Wendy -- see the help page for valid arguments to decideTests ?decideTests Subset the result like a matrix, results[1:20,]. How will you decide on the number '20'? Shouldn't the results reflect some combination of p-value and log fold change? Hope that helps Martin > > Thank you in advance, > Wendy > > Code: > results<- decideTests(fit[,-1], p=0.10, lfc=log2(2),number=20) > Error in decideTests(fit[, -1], p = pval, lfc = log2(foldchange), number = > 20) : > unused argument(s) (number = 20) > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

Dear Wendy, decideTests() tells you which genes satisfy chosen criteria for each contrast in your design. It does not limit the number of hits in advance, and there is no way to do this. It does not rank genes. If you want only a fixed number of top probes, you must use topTable(), which is designed to do this. Best wishes Gordon > Date: Thu, 9 Jun 2011 23:20:10 -0400 > From: Wendy Qiao <wendy2.qiao at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] limit the number of rows in decideTests > > Dear all, > > I have a data set consisted of 4 cell types with each cell type having 3 > replicates. I find the unique signature genes of each cell types using > decideTests (see following). I only want the top, say 20 signature probes > that satisfy my thresholds. I tried to use "number=20" as for the > "topTable" function with "decideTests", but it gave me the an error (see > below). Is there a way that I can define the number of upregulated probes > for outputting in decideTests? > > Thank you in advance, > Wendy > > Code: > results <- decideTests(fit[,-1], p=0.10, lfc=log2(2),number=20) > Error in decideTests(fit[, -1], p = pval, lfc = log2(foldchange), number = > 20) : > unused argument(s) (number = 20) ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}