Hi all, 

Any help would be much appreciated. I have searched for this error and cannot find it anywhere but whats more weird is that I have never experienced this before. 

I have run the following code:

dds<-DESeqDataSetFromMatrix(countData = countdata, colData = sampledata, design = ~ Time_point + Organ)

dds1 <- DESeq(dds, reduced = Organ, test = "LRT")... I am now getting this error:

Error in DESeq(ddsAMIR, reduced = Organ, test = "LRT") : 
  object 'Organ' not found

This is really confusing as the first function (DESeqDataSetFromMatrix works absolutely fine and results check out. The DESeq function then throws up this error. 

A few notes: Sample data... Time_point and Organ are both factors. Countdata are integer and the column names and sample data are in precisely the correct order (again, this has worked before without any problem, so I am not sure what has provoked this issue)

Any help would be much appreciated! Many thanks!

From ?DESeq:

reduced: for  test="LRT" , a reduced formula to compare against, i.e.,
          the full formula with the term(s) of interest removed.
          alternatively, it can be a model matrix constructed by the
          user

And from the examples:

 # an alternate analysis: likelihood ratio test
     ddsLRT <- DESeq(dds, test="LRT", reduced= ~ 1)
     resLRT <- results(ddsLRT)

Which seems pretty clear?