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Currently I am trying to understand DEXSeq package. I have a design tsv file and 7 files which contains Counts. Now would like to run the following command 

library("DEXSeq");

design=read.table("dexseq_design.tsv", header=TRUE, row.names=1);

ecs = DEXSeqDataSetFromHTSeq(countfiles=c("M0.txt", "M1.txt", "M2.txt", "M3.txt", "M4.txt", "M5.txt", "M6.txt", "M7.txt"), design=design, flattenedfile="genome.chr.gff");

The last command gives and error 

Error in class(sampleData) %in% c("data.frame") : 
error in evaluating the argument 'x' in selecting a method for function '%in%':
Error: argument "sampleData" is missing, with no default

What does this error means and how to fix it? While loading the package DEXSeq there was a warning

Warning message:
  replacing previous import by ‘ggplot2::Position’ when loading ‘DESeq2’
Jumaa Khan
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  • Your problem is not related to this warning. It just means that both packages `ggplot2` and `DEXSeq` have a `Position` function, and the one from the latter is masking the one from the former. –  Jan 27 '16 at 07:28
  • so how to fix the error i am facing? – Jumaa Khan Jan 27 '16 at 15:03
  • Without the data, impossible to help further. But according to the error message, `DEXSeqDataSetFromHTSeq` is expecting a `sampleData` you don't have set in your current code. –  Jan 28 '16 at 01:25
  • M0 to M7 contains all the sample data ..Don't know which sample data its requires . – Jumaa Khan Jan 28 '16 at 06:41
  • `DEXSeqDataSetFromHTSeq` has a `sampleData` argument. Set it. And please read the help page. –  Jan 28 '16 at 06:43

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