[BioC] error when estimating Dispersions for count table data in DESeq

[梁芳]

Hello everyone,
I am working in the Beijing Institute of Genomics, Chinese Academy of Science. I used the DESeq to analyze my RNA-seq data, following the instruction file "Dierential expression of RNA-Seq data at the gene level the DESeq package" step by step. It didn't show any error information until I typed the command "cds = estimateDispersions( cds )". The error message was:

Error in if (nr < 2) stop("nrow(modelMatrix) must be >=2.") :
  argument is of length zero

My input file is attached. Could someone let me know what the problem is?
ps. the above error message didn't show up for the test data "pasilla", so there should be no problem with the software.


Following is the code:
library("DESeq");
CountTable = read.table("test.txt", header=TRUE, row.names=1);
Design = data.frame(row.names = colnames(CountTable), condition = c("treated", "treated", "untreated", "untreated"));
cds = newCountDataSet(CountTable, Design);
cds = estimateSizeFactors(cds);
cds = estimateDispersions(cds);


Thanks!
Fang Liang
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