Print Page - EIC and npeak correlation

Title: EIC and npeak correlation
Post by: AmSidebottomIU on July 18, 2011, 06:12:13 PM

Hello

I have a question about the .tsv file "n peaks" column and its correlation with the corresponding EIC.

Sometimes, it appears that they do not correlate, for example- the "n peaks" column will indicate "0" peaks for a group when I can see a peak in the EIC (at 10^4 abundance, which for some peaks indicates "1" and not "0"). Is this caused by a default s/n value or threshold that I have somewhere in my workup?

As always, thank you for any help.

Ashley

Title: Re: EIC and npeak correlation
Post by: Ralf on July 19, 2011, 07:27:06 PM

You see this effect if these features were not initially detected during feature detection ( i.e., they were below S/N threshold),
but filled in later by fillPeaks.

Also see
http://metlinwiki.scripps.edu/mediawiki ... of_samples (http://metlinwiki.scripps.edu/mediawiki/index.php/How_is_it_possible_to_have_npeaks_values_higher_than_the_total_number_of_samples)

Title: Re: EIC and npeak correlation
Post by: AmSidebottomIU on July 21, 2011, 08:32:42 AM

Interesting- so I should follow the npeaks read-out when the two (EIC and npeaks) don't agree?

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Software => R => XCMS => Topic started by: AmSidebottomIU on July 18, 2011, 06:12:13 PM