Hi Paul, reading the code you wrote I think I understand what you mean but I haven' t understand the way to use the function you wrote, because is not clear in my mind how to extract a scan from an xcmsSet object :oops: .
Hi to everybody, I'm setting up an xcms object using the matchedFilter algorithm. So, reading the Smith's paper (XCMS: Processing Mass Spectrometry....) I'm adjusting s/n and fwhm parameters to obtain the best result.
My question is about the red horizontal line: I think is regulated by the s/n so, the higher is the s/n the higher is the red line. Is it right?? Is the red line used as baseline to integrate the signal?? How it is calculated the s/n ratio?? RMS or Peak to peak??
What I meant was have you tried analysing the same dataset on XCMS Online, to see if it works there ?
Hi I tried to use xcms online and it works. So the problem is in my workstation. Have you ever tried to use xcms with R 2.14?? Uninstall and re-install the downgraded version of R is the very last option. :cry:
Do you have any further suggestion??
Best
EDIT I also tried on my home computer and all works fine. The session info on my home pc is:
loaded via a namespace (and not attached): [1] graph_1.32.0 grid_2.14.1 Hmisc_3.9-0 igraph_0.5.5-3 lattice_0.20-0 [6] RBGL_1.30.1 tools_2.14.1 > I see the main difference is the xcms version that in the home pc is 1.30.0.
Where can I download these old version to try it on my work pc??
Hi to all and good year! I have had a problem running fillPeaks. Controllo10 Error in checkSlotAssignment(object, name, value) : "scantime" is not a slot in class “NULL”
My data set is made up of 60 negative control and 15 positive control. Is correct to use minsamp=10 that is 2/3 of the positive control? My data were aquired with Agilent LC/qTOF.
the xcmsSet function says: Error in `row.names<-.data.frame`(`*tmp*`, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': ‘’ .
If I see the files object, I do not see any duplicate.
Hi, I am a mac user (OS X 10.5. I have already upgraded R to 2.14.0 to use the last relese of xcms and now I have some problem to load it. When I try to load xcms the R consol say:
library(xcms) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Users/riccardoromoli/Library/R/2.14/library/xcms/libs/x86_64/xcms.so': dlopen(/Users/riccardoromoli/Library/R/2.14/library/xcms/libs/x86_64/xcms.so, 6): Library not loaded: /usr/local/lib/libnetcdf.7.dylib Referenced from: /Users/riccardoromoli/Library/R/2.14/library/xcms/libs/x86_64/xcms.so Reason: image not found
Errore: package/namespace load failed for ‘xcms’
I think the error is the absence of ibnetcdf.7.dylib. Do you have any idea how can I correct this error??
My question is about the usage of the getIsotopeCluster function, in particular how can I extrapolate only the information about the $peak slot of all my sample and collect them into a data frame??
Hi to everybody, I have somethings in my mind that is unclear about the interpretation of the result obtained using the xcms package for metabolomic data analysis.
Because I have more than two classes I haven't used the diffreport function to extract the most significant peaks according to their ANOVA p-value, but I wrote some code to do this. So I found a small number of signal that are significantly different among the treatment and I use this for the multivariate statistical analysis.
Furthermore the next step was to try to understand if the significative peaks have a "name and surname". To do this I extracted the m/z information from the peak list using the groupnames function and I used the Metabolite Search engine directly from my web browser. I adjusted the ppm error and the polarity.
Now the question: how about the charge state parameter?? In particularly I tried different charge state option: M+H, M+Na, M+K, M+H-H2O... and I studied the results obtained, trying to understand which are the different signal obtained crossing the different data report. For example if the signal 490.1765 m/z has no positive hits with the M+H option, but have a positive hit with the M+Na option, I conclude that is a sodiated adduct instead of a protonated adduct.
Is a correct way to try to identify a metabolite?? Why the diffreport approach has only an M+H information?? Should I use a de-isotoping function to be sure I work only with M+H signal?? Is possible to do this with xcms??
Best
P.S. Sorry for my bad English :oops: I hope you can understand the question/s.
I have already upgraded R to 2.14.0 to use the last relese of xcms and now I have some problem to load it. When I try to load xcms the R consol say: