Open denisbruno1 opened 5 years ago
Hi there,
Thank you for using DeepVirFinder!
Are all the predicted contigs have p-value=0.0? Or you selected those contigs with value 0.0 and estimate the q-value only for those?
We recommend estimating q-values for all contigs and then choose those contigs with small q-values as the predicted viral contigs.
If only the contigs with p-value=0.0 are fed into the q-value estimation function, the distribution may violate their model assumption, which can be the reason that causes the error. See a similar discussion in the qvalue package: https://github.com/StoreyLab/qvalue/issues/9
Thank you!
Jie
Thank u for the agility in the answer! All the predicted contigs have p-value=0.0, I am thinking that this is a kind of my error. I tried to do the methodology applied in StoreyLab, but did not work, exactly because the p-values are equals to 0, so the package o qvalue inform the follow
p-values not in valid range [0, 1].
The curious is that not only in mine dataset occurs this, but in CRC_meta test too. Had I fail in installing something correctly?
Thank you for providing the details. Is your data mostly from viruses? If not, it is strange that all contigs have p-value=0.
How about the crassphage example? what is the score you get?
python dvf.py -i ./test/crAssphage.fa -o ./test/ -l 300
The score should be something like, name len score pvalue gi|674660337|ref|NC_024711.1| Uncultured phage crAssphage, complete genome 97065 0.9978806972503662 0.004702016768638115
Jie
From: denisbruno1 notifications@github.com Sent: Wednesday, March 6, 2019 3:54:56 AM To: jessieren/DeepVirFinder Cc: Jie Ren; Comment Subject: Re: [jessieren/DeepVirFinder] Error in calculating q-value (#2)
Thank u for the agility in the answer! All the predicted contigs have p-value=0.0, I am thinking that this is a kind of my error. I tried to do the methodology applied in StoreyLab, but did not work, exactly because the p-values are equals to 0, so the package o qvalue inform the follow? p-values not in valid range [0, 1]. The curious is that not only in mine dataset occurs this, but in CRC_meta test too. Had I fail in installing something correctly?
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When I tried this, p=0.0 again, like bellow
name len score pvalue gi|674660337|ref|NC_024711.1| Uncultured phage crAssphage, complete genome 97065 0.99788069725 0.0
Data scientist Sean Hackett @shackett has provided a resolution to this error.
Please visit: https://github.com/StoreyLab/qvalue/issues/19
Though I don't understand much of the statistical know-how, it worked for me.
Best
Hi! I am using DeepVirFinder to test RNA-seq experiments for virus discovery. But when I try calculate the q value, using both my dataset and the CRC_meta test, appears the following error?
Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are not allowed.
One detail are the p values = 0.0 for all the matchs. How can I fix this?