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Topics
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Topics - dlforrister
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CAMERA / Error in x$membership
I am trying to annotate my peak list using Camera. I get the following error on the first step:
> xsa <- xsAnnotate(xs=xset4,polarity="negative")
Error in x$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
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XCMS / retention time correction for individual sample classes
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!
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XCMS / saving xcmsSET object to CDF or mzXML files
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