Cummerbund Expressionbarplot Na/Infinite Error

Question

[Andrew Watson]

Hi all,

I am having trouble with the expressionBarplot function on cummeRbund and was wondering if anyone could help me.

I want to look at the expression plot of a manually created geneset. I have worked through several already without any problems, but this particular set is pulling up the below error when I try to generate a barplot:

Error in seq.default(min, max, by = by) : 'to' cannot be NA, NaN or infinite

I have been through the diffData section for the geneset and removed any genes with -inf values for log2_fold_change from the analysis but this was unsuccessful. I also tried setting a pseudocount and log transforming the data without any luck.

I have been unable to find any other potentially problematic NA, NaN of infinite characters but I'm not really sure where exactly I should be looking for them to begin with as I don't really know which data files expressionBarplot is actually reading in.

Does anyone have a better idea of where I might find the problem characters, or has anyone encountered the same problem before? I might just be being a little thick here!

Thanks!

Answer 1

[Andrew Watson]

Just to confirm I have been managed to solve this in case anyone else encounters the problem.

As I have annotated against a reference genome I have some cases where zero expression has been detected under either of the conditions I am studying.

I used the matrix of the fpkm values (from fpkmMatrix) and removed every gene that had zero expression in both of the conditions I am studying from the dataset.

I'm not sure why pseudocount didn't deal with this. I had expected it to, hence not trying this earlier. Possibly because both conditions had zero expression data. Either way this appears to have removed the offending characters.

Cheers!

[mk234]

Hello Andrew,

I am currently encountering this problem while trying to use the dispersionPlot function. My call is:

---

disp<-dispersionPlot(genes(cuff))

disp

---

And then I receive the error:

---

Error in seq.default(min, max, by = by) : 

  'from' cannot be NA, NaN or infinite

---

I removed every gene from fpkmMatrix, but then the dispersionPlot() method would not accept the resultant data frame as its input. How would you modify the input in this case?

Thank you

[AlanT]

Same problem for me. Did you found a solution ?