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Question: Need to read in DEXSeqResults object to R from csv
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gravatar for cjm
9 weeks ago by
cjm0
cjm0 wrote:

Hello,

I ran DEXSeq on a linux based cluster and saved the DEXSeqResults object as a .csv file to run locally for further analysis and visualization.  When I read in the .csv to R, I am able to see it appear properly in the Data Environment, but none of the commands that should run from this work.  I have updated bioconductor and all packages along with my version of R.

Example:

> mcols(dxr1)$description
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘mcols’ for signature ‘"data.frame"’

or

> DEXSeqHTML(object=dxr)
Error in DEXSeqHTML(object = dxr) : 
  is(object, "DEXSeqResults") is not TRUE

I need to run the main part of DEXSeq on the cluster due to memory issues, but would like to be able to analyze and visualize locally.  Any help would be appreciated.

Best,

Christina

ADD COMMENTlink written 9 weeks ago by cjm0

Hi Christina, can you post the complete code that you are using along with the output of your sessionInfo()?

ADD REPLYlink written 9 weeks ago by Alejandro Reyes1.6k

The most common and recommended way to save R objects, move them to a different computer and open them there again are the save and load functions in R. It looks like that the CSV file you saved from the cluster only contains part of the DEXSeqResults object, and what you loaded is not a DEXSeqResults object but just a data.frame, for which what you are trying to do (DEXSeqHTML) cannot work.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Wolfgang Huber13k
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