Error: could not find function "DESeqDataSet" from DESeq2

Question

[imrankhanbioinfo]

Hi Guys, I am encountering an error when creating dds (DESeqDataSet). I was running DeSeq one day back everything was good but now I am having some issues like not able to find some function. I suspect its coz of my R studio (Ver. 1.2.5033). What do you think? After loading some packages I can't access functions associated with them. Best: Imran

require(DESeq2)
dds<-DESeqDataSetFromMatrix(countData=mycounts, 
                            colData=metadata, 
                            design=~Condition, 
                            tidy=TRUE)

Error in DESeqDataSetFromMatrix(countData = mycounts, colData = metadata,  : 
  could not find function "DESeqDataSetFromMatrix"

[Kevin Blighe]

Hi Imran, please show the output of sessionInfo() ? Just also check to see if DESeq2::DESeqDataSetFromMatrix(...) functions ?

[Asaf]

Also, require doesn't throw an error, can you try library insead?

Answer 1

[imrankhanbioinfo]

Thank you very much for your help. It works now. I used sessioninfo() and get my answer. There was some issue with my Rstudio and the complete installation of DeSeq2. Some packages were unable to install with the DeSeq2, so I have to do it separately.