Question: What to do when a bug is found in a BioConductor package (Glimma)
0
gravatar for Samuel
12 weeks ago by
Samuel0
Samuel0 wrote:

As far as I can tell, I have found a bug in Glimma.

The following code

library(Glimma)

DE <- as.data.frame(cbind(202197.7, -1.410116), byrow=T)

colnames(DE) <- c("baseMean", "log2FoldChange")
DE$sig <- 1


glMDPlot(x=DE, xval="baseMean", yval="log2FoldChange", counts=NULL,
         anno=NULL,samples=NULL, group = NULL, status=DE$sig, 
         side.main = "baseMean",html="One_Gene_from_vector_final",
         display.columns = c("baseMean","log2FoldChange"))

produces the following graph :

glimma plot

As you can see, the baseMean is rounded (incorrectly) to 202200.

What is the etiquette in this case? Should I email the developers directly?

software error glimma • 124 views
ADD COMMENTlink modified 12 weeks ago by Gordon Smyth39k • written 12 weeks ago by Samuel0

Thanks for the bug report Samuel. As Gordon mentioned, I would prefer bugs be submitted through Github issues. The reason for the bug is that I've rounded all values to 4 significant places to avoid values with tens of digits, it's clear that this causes confusion for large numeric values so I'll update the rounding strategy soon.

ADD REPLYlink written 12 weeks ago by Shian Su20
Answer: What to do when a bug is found in a BioConductor package (Glimma)
1
gravatar for Gordon Smyth
12 weeks ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

If you type packageDescription("Glimma"), or visit the Glimma landing page at the http://bioconductor.org/packages/Glimma, you will see that Glimma has an issues site for reporting bugs or other issues:

https://github.com/Shians/Glimma/issues

I'm not sure that rounding would be considered a bug though.

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by Gordon Smyth39k
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