DESEq2 error following reference-based RNA-Seq tutorial

1

Hi Galaxy,

I am trying to run the DESeq2 tool step, following the reference-based RNA-Seq data analysis tutorial. I have 1 factor, 6 samples, which are performed in triplicates so a total of 18 sequences within one collection, as per the tutorial, and want to compare the differential gene expression between the 6 samples. When I identify each sample as a factor level with their corresponding tags ive created I get an error. When I run the tool with datasets based on levels I also get an error.

When I change the fit type to ‘local’ instead of ‘parametric’ and the estimesizeFactor as ‘iterate’ I get the following message.

using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates: 3 workers
mean-dispersion relationship
Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, :
newsplit: out of vertex space
Calls: DESeq … estimateDispersionsFit → localDispersionFit → locfit → lfproc
There were 17 warnings (use warnings() to see them)

Please help me.

2

Hi @emily-kwan
have we sorted this error through Galaxy Australia support or it is still an issue after removal of the control samples?
You can add server tags to post on the forum. It helps to know what server was used.
Kind regards,
Igor