DESeq2 error in design~ code
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@0c947827
Last seen 5 weeks ago
Morocco

Hi everyone I need to run Deseq2, but when I try to run this part of command the following error message appears.

**Error in DESeqDataSet(se, design = design, ignoreRank) : 
  design has a single variable, with all samples having the same value.
  use instead a design of '~ 1'. estimateSizeFactors, rlog and the VST can then be used
De plus : Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  1 duplicate rownames were renamed by adding numbers**

I am new to R and DESeq2, Please anyone could hepl me to fix this error. Thank you very much

DESeq2 • 291 views
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removed EnhancedVolcano tag

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@james-w-macdonald-5106
Last seen 22 hours ago
United States

The error tells you how to fix it. One of the best skills you can cultivate is the ability to read and interpret the messages that you get from R (or any software, for that matter).

The error says that the variable you are using has only one level (e.g., all your samples are the same type), in which case you just need to use

design <- model.matrix(~1)

But that is a pretty rare thing! An alternative is that you do have different levels (e.g., you have two or more types of samples), in which case you need to redo your design matrix, using the factors that describe your sample types.

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Thank you very much

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