Galaxy error in EdgeR and DEseq2

Hi, I am running EdgeR and got following errors. Can you please instruct me on how to solve these issues

  1. Error in .rowNamesDF<-(x, value = value) :
    duplicate ‘row.names’ are not allowed
    Calls: row.names<- -> row.names< -> .rowNamesDF<-
    Warning message:
    non-unique values when setting ‘row.names’: ‘…data.37……ali
  2. Error in quantile.default(x, p = p) :
    missing values and NaN’s not allowed if ‘na.rm’ is FALSE
    Calls: calcNormFactors … .calcFactorQuantile -> apply -> FUN -> quantile -> quantile.default

Further, I got following message in DEseq2

  1. estimating size factors
    Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, :
    every gene contains at least one zero, cannot compute log geometric means
    Calls: DESeq … estimateSizeFactors -> .local -> estimateSizeFactorsForMatrix

I am in a really tight schedule. So that it will be great if I can get information asap.
Thank you
Randika Yapa

1 Like


Start by double-checking your usage against the advice in this FAQ and the linked tutorials at the end of it. The tool forms also have example inputs and more useful help.

It appears you had a problem getting counts assigned to genes.

Also, make sure you are using the most current version of all tools. Many have had bug fixes and enhancements. This might involve updating a workflow, if you are using one.


Is there any prediction when the galaxy server will be up

Thank you


We are working towards getting it up asap. If we know more, we will post it at

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Just a bit more detail also in this post: upload from FTP gives: bad request (400)

(How to navigate the status page, link to current status, etc)