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Topics - JHela001

1
XCMS / Get fold, p-value for set of EIC m/z values
Hi everyone,

I am trying to find a simple way to export integration data for a set of EIC's from my data in metabolomics.

I have a table of ~50 EIC's that I'd like to simply extract their fold change, p-value, q-value from my data sets. Ideally I'd also like to export whether there are outliers but this isn't necessary at this moment.

Has anyone developed a script to do just this, without looking for all the significantly different peaks?

I am not exceptionally familiar with R. We have been using the simple script to look at all the differences:

Code: [Select]
library(xcms)
files <- list.files(recursive = TRUE, full.names = TRUE)
xset <- xcmsSet(method = "centWave", files = files, ppm = 15, peakwidth = c(6,40), nSlaves=3)
xset <- group(xset)
xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden")
xset2 <- group(xset2, bw = 8)
xset3 <- fillPeaks(xset2)
reporttab <- diffreport(xset3, "x", "y", "x_vs_y", 2500, metlin = 0.15, h = 480, w = 640)

Thanks in advance
2
metaXCMS / OTHER common features (Treatments 1, 2 NOT 3)
When "Export common features" tab is clicked, it exports a file with the common features of all 3 of my treatments.

This is interesting and useful, but I also want to look exclusively at what is common in treatments 1&2 (not 3), 2&3 (not 1) and 1&3 (not2).

Is there a convenient way to do this?

Thanks.