P-Value of zero in common features? May 21, 2012, 04:13:08 AM I am observing a p-value of zero in my metaXCMS common features? It is obviously incorrect to report this p-value..Is there a certain number of decimal places which metaXCMS reports? Are these values indeed significant or not? Has anyone else seen this?Thanks in advance.

Re: P-Value of zero in common features? Reply #1 – May 21, 2012, 11:16:56 AM metaXCMS does not modify the p-values of your experiments.Do you have p-values of zeroe in the diffreports that you import into metaXCMS ?

Re: P-Value of zero in common features? Reply #2 – May 22, 2012, 07:18:21 AM Hi Ralf,I have checked through the diff reports and the highest P-value for feature lowest ranked feature in each subject is 0.98 or so. There are no 0 values? The highest ranked common feature is 166.021416 m/z with the following results: Subject A (control vs. intervention) UP(fc=3.7,pval=0), Subject B (control vs. intervention) UP(fc=2.3,pval=0.00018), Subject C (control vs. intervention) UP(fc=3.1,pval=0). I have checked for this feature in each individual diff report and I get the following p-values Subject A (p=5.77E-07), Subject B (p=0.000184097), Subject C (p=2.51E-06). Any idea why I might be getting zero values like this in the common features? I am filtering by 0.01 p-value, 2 fold change, then m/z tolerance of 0.005 and an RT tolerance of 20 seconds? Don't know if this clarifies it is not in all of the common features just some.Thanks for your help,Will

Re: P-Value of zero in common features? Reply #3 – May 23, 2012, 05:15:43 PM The p-value is rounded to 5 digits using R's round() function.It seems that round() just outputs zero for very small numbers.The p-value of that particular feature must be very small, have you tried looking it up in the original diffreport for subject C ?I guess I could make the number of digits an option.