Prefilter Parameters

Topic: Prefilter Parameters (Read 5942 times) previous topic - next topic

Prefilter Parameters

June 14, 2011, 02:10:00 PM

Hello,

I am following parameters optimized for our LC/MS datasets, and in R, this parameter is

prefilter=c(1,30)

In the web-based version of XCMS, would this be prefilter intensity and prefilter peaks?

Thanks very much!

Majda

Re: Prefilter Parameters

Reply #1 – June 14, 2011, 02:50:30 PM

Correct

XCMS:
prefilter=c(k,I). Prefilter step for the first phase. Mass traces are only retained if they contain at least k peaks with intensity >= I.

XCMS Online:

prefilter peaks = k
prefilter Intensity = I

Re: Prefilter Parameters

Reply #2 – June 15, 2011, 08:23:43 AM

Thank you Ralf! I appreciate your responses!

Majda

Re: Prefilter Parameters

Reply #3 – June 15, 2011, 08:28:02 AM

Ops, just noticed you wrote:

prefilter peaks=k
prefilter peaks=l

The second is supposed to be prefilter intensity, correct?

Thanks!

Majda

Re: Prefilter Parameters

Reply #4 – June 15, 2011, 08:51:02 AM

Yes, it is.

I just edited it.
Ralf.

Re: Prefilter Parameters

Reply #5 – June 15, 2011, 02:14:27 PM

Thank you!

Majda