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Messages - TimB90

1
XCMS / Odd group() / minfrac behavior.
Hello folks,
I found a (for me inexplicable) phenomenon when working with the group.density function of XCMS.
I played a little with the minfrac and minsamp arguments and set both to 0, having in mind that this should be some kind of unbiased grouping (i.e. getting for example features that  occur only in one replicate).
I obtained 1022 features using the faahko data set.
Code: [Select]
library(faahKO)
Frac0Samp0<-group(faahko, minfrac = 0, minsamp = 0)
nrow(Frac0Samp0@groups)
## 1022
The same procedure for the default group() settings (minfrac = 0.5, minsamp = 1)
Code: [Select]
Frac50Samp1<-group(faahko, minfrac = 0.5, minsamp = 1)
nrow(Frac50Samp1@groups)
## 407
So far so good, but when I compared the mzmed values of the two datasets with setdiff(), I found one value that did not appear in the "unbiased" xmcsSet object Frac0Samp0.
Code: [Select]
setdiff(Frac50Samp1@groups[,"mzmed"], Frac0Samp0@groups[,"mzmed"])
## 592.4473
As soon as I set minfrac to 0.5 and leaving minsamp = 0 the missing value/feature is appearing again.
Has someone an idea why this is happening or how I could do a real unbiased grouping?
Kind regards,
Tim
2
XCMS / Re: peak shape/symmetry?
Hello,
I see that this post is rather old, but still it is kind of perfect for my question. Is there a possibility to get a readout of the peak meta data (for gauss fit) if i chose xcmsSet(...) for batch processing?
Code: [Select]
verbose.columns=TRUE
I know that if I use the sleep function together with xcmsSet (verbose.columns=TRUE) I get at least a pdf with the peak shape-related data, but I'd prefer an excel readable file to filter out peaks with an odd shape. I can imagine that this is kind of a problem since the xcmsSet function is meant for analyzing various rawfiles and to group detected features of every rawfile.
It could be helpful if at least the peak shape meta data of the feature with the highest intensity of the group could be returned in a csv-file. I hope you get my question and thanks for your help,
Tim