Question

DEsingle differential-expression analysis

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5.0 years ago

Lucy ▴ 140

Hi,

I am running DEsingle (https://pubmed.ncbi.nlm.nih.gov/29688277-desingle-for-detecting-three-types-of-differential-expression-in-single-cell-rna-seq-data/) to compare two clusters of cells identified by Smart-seq2 scRNA-sequencing. I have filtered the genes before running DEsingle to retain only genes expressed in at least 10% of cells from one of the two clusters (5379 genes retained). DEsingle outputs the results but I get the following warning message. How concerned should I be about this message and should I trust the results?

Warning message: In MLE(ll3, start = listeta.mu = eta.mu, eta.sigma = eta.sigma, : possible convergence problem: optim gave code=1 function evaluation limit reached without convergence (9)

Many thanks,

Lucy

differential-expression analysis scRNA-seq • 1.3k views

ADD COMMENT • link 5.0 years ago by Lucy ▴ 140

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As this is a very specific question towards a Bioconductor package you might want to cross-post it to their support forum using DESingle as a tag. Maybe the developers watch this tag and therefore get notified.

In general you should post the relevant code and if possible some data to reproduce the issue.

ADD REPLY • link 5.0 years ago by ATpoint 85k

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Ok thank you. I did try asking on their GitHub but I haven't had a response.

ADD REPLY • link 5.0 years ago by Lucy ▴ 140

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There are many tools for DEG in scRNA-seq data. For the sake of getting expert help in case of trouble you might consider switching tools. Not saying DEsingle is not good but in such an non-standardzed field as scRNA-seq you might benefit from well-maintained tools (again not saying DEsingle is not maintained, in fact I do not know) but you might think about it.