Question: qvalue package throws error when used on any p-values but hedenfalk example
1
20 months ago by
ilikescience110 wrote:

I've been trying to get the qvalue package to work for me. However, when I put in a vector of p-values I get the following error:

Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are not allowed

I have tried inputting the p-values in various ways.

Consider a vector of p-values such as .0009, .02, .423, .012, .003 ... I create a list called p.values containing a numeric vector named V1 of these values.

Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are not allowed

I try qvalue(c(.0009, .02, .423, .012, .003), fdr.level=.05) and obtain the same error.

the same happens if I leave out fdr.level=.05 and just run qvalue(p.values$V1) or qvalue(c(.0009, .02, .423, .012, .003)). I however run the example qvalue(hedenfalk$p) and it works no problem... I've tried reloading the package as well as uninstalling-reinstalling it.

There are no missing or infinite values, so I don't know what the problem could be.

Anyone have an idea what's going on?

qvalue • 1.4k views
modified 20 months ago by Storey, John D.60 • written 20 months ago by ilikescience110

I also had this problem. I have 816 P-values, seems that there are many p-values that are close to 0, and this causes the error too.

Answer: qvalue package throws error when used on any p-values but hedenfalk example
1
20 months ago by
United States
Storey, John D.60 wrote:

You don't have enough p-values to warrant estimating pi0, so include the argument lambda=0.