Ensure p-values are numeric before sorting #2
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The p variable at some point became a list of character strings that when sorted, do not sort properly due to the number of digits in the p-value. For instance, a p-value of 0.999984 would be sorted as being larger than 0.9999864 even though it's numeric value is smaller. I believe this has the effect of increasing the q-values from the qvalue function because the list is no longer in order, so larger q-values may sometimes be treated as being smaller. This will then decrease the number of significant associations output by WGCNA.
ryananeff
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The p variable may at some point become a list of character strings that when sorted, do not sort properly due to the number of digits in the p-value. For instance, a p-value of 0.999984 would be sorted as being larger than 0.9999864 even though it's numeric value is smaller.
I believe this has the effect of increasing the q-values from the qvalue function because the list is no longer in order, so larger q-values may sometimes be treated as being smaller. This will then decrease the number of significant associations output by WGCNA.
Therefore, either ensure that the p-values are numeric before sorting or cast it to a numeric type.