Question: DESeq2 Exploratory analysis of a single timepoint vs control
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gravatar for csteely4
6 months ago by
csteely40
csteely40 wrote:

I'm interested in comparing the levels of certain transcripts from an experimental time point versus a control time point. However, whenever I run DESeq2 on the counts table, it throws this error:

estimating size factors estimating dispersions Error in checkForExperimentalReplicates(object, modelMatrix) :

The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples as replicates was deprecated in v1.20 and no longer supported since v1.22.

Calls: DESeq ... estimateDispersions -> .local -> checkForExperimentalReplicates Execution halted

Is there an easy work around for this? I'm simply looking to see if there's a relative change from time point to time point.

Thanks for any help you can give.

deseq2 • 351 views
ADD COMMENTlink modified 6 months ago by Michael Love25k • written 6 months ago by csteely40
Answer: DESeq2 Exploratory analysis of a single timepoint vs control
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gravatar for Michael Love
6 months ago by
Michael Love25k
United States
Michael Love25k wrote:

You can use a design of ~1

ADD COMMENTlink written 6 months ago by Michael Love25k
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