[BioC] help with DESeq

[Simon Anders]

Dear Nirmala

> We have 4 cases and 5 controls. We would like to add RIN number as one of the covariates to the data analysis. Here is my code which gives errors:
>
>> countsTable=read.table("4Cases_5Controls_counts.txt",header=TRUE)
>> cdsFull<- newCountDataSet( countsTable, nisc1Design )
>> cdsFull<- estimateSizeFactors( cdsFull )
>> cdsFull<- estimateDispersions(cdsFull,"pooled")
>> Error in rowSums(sapply(tapply((1:ncol(counts))[replicated_sample], factor(conditions[replicated_sample]),  :
>>     'x' must be an array of at least two dimensions

At the very least, tell us what is the variables you use to construct 
the CountDataSet, i.e., post the content of 'nisc1Design' and the head 
of 'countsTable'.

   Simon