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mhammell-laboratory / TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
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DESeq error #37

Closed CodyS5 closed 5 years ago

CodyS5 commented 5 years ago

Hello,

When working with a single control and multiple treatments, I get clean output from TEtranscripts. However, when working with a single treatment bam and a single control bam I get the following error message from DESeq2:

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 INFO : Done

Is there a work around for this, or do you have any recommendations? My data is moving through time points, so ideally I would be able to compare each new timepoint to the last.

Thank you.

olivertam commented 5 years ago

Hi,

Unfortunately, this is a limitation put in place by DESeq2 as of version 1.22.0 (see here). A possible workaround is to use an older version of DESeq2 (as the error message indicates, treating samples as replicates is no longer supported in v1.22, so version <=1.21 should at least handle it). It might also be worth raising this question to the authors of DESeq2 (recommended approach) to see if they have any recommendations on how best to address this issue.

Thanks.

CodyS5 commented 5 years ago

I kind of figured that might be the best way around it, but I thought I'd ask in case you had seen this before. Thank you for the help!