DEXSeq help - error: model matrix not full rank
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@greenhawmatt-12843
Last seen 7.7 years ago

Hi all,

I am new to using DEXSeq and I could use some help from someone familiar with it. 

I am following the vignette with my dataset in stepwise fashion. My error occurs during this step "dxd = estimateDispersions( dxd )". The error message suggests using "ddx <- estimateDispersionsGeneEst(ddx)". After trying that I get the error message saying that model matrix is not full rank. 

My experiment table looks like this:

  condition
S1 disease
S2 healthy

And my design formula for DEXSeqDataSetFromHTSeq is: design = ~ sample+exon + condition:exon

Any help is much appreciate. Thank you. 

Best,

Matthew

dexseq • 1.2k views
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Hi Matthew. The error is being produced because the experiment does not seem to have replicates. Sorry, DEXSeq does not support such cases.

Alejandro

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Hi Alejandro,

Thanks for your reply. I tried running DEXSeq with replicates but I still get the same error about a non full rank matrix. Can you help with this?

<caption>matrix before "estimateDispersionsGeneEst"</caption>
sample condition exon sizeFactor
<factor> <factor> <factor> <numeric>
S7_1 disease this 1
S7_2 disease this 1
S8_1 healthy this 1
S8_2 healthy this 1
S7_1 disease others 1
S7_2 disease others 1
S8_1 healthy others 1
S8_2 healthy others 1

 

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Would you include the full code that generates the error and the output of your sessionInfo() ?

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