Error in DESeq "object" not found
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@a-14337
Last seen 1 day ago
United Kingdom

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!

 

 

deseq2 LRT reduced model • 406 views
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@james-w-macdonald-5106
Last seen 17 hours ago
United States

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?

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I'd like the term of interest Organ removed though... So it should recognise that I am trying to do this.. Especially as it does in the full model design for the first function?

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I agree that it would be sweet if R would be able to read your mind and know what you want it to do, but it doesn't work that way. Hence the help pages.

Do you know what is meant by the word 'formula' in the help page, particularly given the example that contains one? If not, you should look at ?formula, the help page for formulas.

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