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Topics - dlforrister

1
metaXCMS / fill peaks, check raw data
I am using metaXCMS to generate a large peaktable with all features found from many different species of plants. I first processed these individual species using XCMS, RTCor,grouping etc. I then used metaXCMS generate the all species peaktable. I am concerned that this method will generate a lot of false negatives if a feature is not picked up by the original peak picking parameters. I'd like to use fillpeaks or getPeaks to fill out the all species peak table. Anyone done this or know of a way?
2
CAMERA / Error in x$membership
Hi all,

I am trying to annotate my peak list using Camera. I get the following error on the first step:

> xsa <- xsAnnotate(xs=xset4,polarity="negative")
Error in x$membership : $ operator not defined for this S4 class


This error occurs on both R 3.1.3 and R 3.1.2

Some googling indicated that the issue is probably due to the using a newer version of R and of igraph 1.0.1. I've tried rolling back to previous versions of both R but have had issues.

Any suggestions?

Thank you,

DF
3
XCMS / retention time correction for individual sample classes
We are working with xcms to analyze plant secondary metabolites for different species of closely related plants using a waters G2QTOF UPLC-MS.

We have a question regarding correcting for retention time shifts across many samples with a limited number of shared features. It is possible individual sample classes will share only a single internal standard.

Each species makes up a sample class with 5 individuals as replicates per class. However, given the total number of samples, data acquisition has occurred over time and some RT shifts have been observed on the order of (+/- 1.0 min)

Our understanding of the retcor-loess and Obiwarp methods indicates we will have issues aligning all sample classes because there are not enough shared features. Similarly, obiwarp chooses a single sample to align the rest with such a diverse set of samples the chosen sample will not be representative of all other samples. 

Does retcor() work by aligning samples within a sample class first then aligning across samples classes?

Is it possible to apply RT correction to each sample class individually then merge or save these corrected xcmsSET objects for a general analysis of all samples?

Thank you for your help!
4
XCMS / saving xcmsSET object to CDF or mzXML files
Is it possible to save rt corrected xcmsSET objects to CDF or mzXML files without discarding rt correction data?

We aim to compare many sample classes, with different metabolites in each class. Thus, few features are shared across classes and therefore retention time correction methods (i.e obiwarp) might not be effective. In fact the only feature shared across all samples is a single internal standard we used to check RT shifts.

Is it possible to apply rt correction to each sample class individually then save and or merge xcmsSet objects in order to perform a final general comparison between classes?


Thank you all,

DF