gravatar for alwhiteh

1 day ago by

Hello,

I am analyzing some ATAC-seq from flies using Diffbind3.0.8 and EdgeR.

I initially ran dba.analyze() with the default peak size of 401 and was able to graph the results using dba.plotMA and dba.plotVolcano when my contrasts were evaluated using both EdgeR and DESEQ2.

After resizing the peaks to 100 (as recommended in the update), I am able to plot the results using DESEQ2 without any issues, but the EdgeR analysis seems to be causing some errors. Specifically, when I use dba.plotMA, I get the following error:

Error in plotfun(res$Conc, res$Fold, pch = 20, cex = cex, col = crukBlue,  : 
  is.finite(xlim) are not all TRUE

When trying to export the EdgeR object using the following code:

dba.analyze(Age_ATAC, method = DBA_EDGER, bRetrieveAnalysis = T)

I encounter this error:

Unable to return DEObject: design must be present, and analysis run.

Lastly, when trying to save the EdgeR output using dba.report(), I encounter the following error:

Error in .Call2("C_solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  In range 11691: at least two out of 'start', 'end', and 'width', must
  be supplied.

Is there something wrong with my files (that DESEQ2 automatically filters out?), or is this a bug in the Diffbind3 update?

Thanks in advance,

Alex



Source link