Search
Question: qvalue package throws error when used on any p-values but hedenfalk example
0
gravatar for ilikescience1
7 months ago by
ilikescience10 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?

ADD COMMENTlink modified 7 months ago by Storey, John D.60 • written 7 months ago by ilikescience10
1
gravatar for Storey, John D.
7 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.

ADD COMMENTlink modified 7 months ago • written 7 months ago by Storey, John D.60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 147 users visited in the last hour