Galaxy error in EdgeR and DEseq2

usegalaxy.org support
1

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<-.data.frame → .rowNamesDF<-
    Warning message:
    non-unique values when setting ‘row.names’: ‘HISAT2.on.data.38..data.37..and.data.50..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

2

@randikaqut

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.

https://galaxyproject.org/support/

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.

3

Hello,

Is there any prediction when the galaxy server will be up

Thank you

Randika

4

We are working towards getting it up asap. If we know more, we will post it at https://status.galaxyproject.org

5

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)