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CAMERA / Feature Warning and Hanging at graph cross linking
I'm running into some problems with the annotate() wrapper function in the CAMERA package. I am using CAMERA to annotate 686 LC/MS samples hoping to eventually extract the isotope and "pseudospectra" data from the final object.
I am using a xset that I converted from a XCMSnExp object as such after peak detection, grouping, rt correction, regrouping, and peak filling in xcms.
Code: [Select]
xset <- x_filled
xset <-as(xset, "xcmsSet")
I run this to avoid this error: https://support.bioconductor.org/p/69414/
Code: [Select]
imports = parent.env(getNamespace("CAMERA"))
unlockBinding("groups", imports)
imports[["groups"]] = xcms::groups
lockBinding("groups", imports)
Then my function:
Code: [Select]
xset_a = annotate(xset,
quick=FALSE,
sample=NA,
nSlaves=16,
sigma=6,
perfwhm=0.6,
cor_eic_th=0.75,
graphMethod="hcs",
pval=0.05,
calcCiS=TRUE,
calcIso=TRUE,
calcCaS=FALSE,
maxcharge=4,
maxiso=4,
minfrac=0.5, # 0.25?
psg_list=NULL,
rules=NULL,
polarity=subset.polarity,
multiplier=3,
max_peaks=100,
intval="into",
ppm=2.5,
mzabs=0.0015
)
I get this output:
Code: [Select]
Starting snow cluster with 16 local sockets.
Run cleanParallel after processing to remove the spawned slave processes!
Start grouping after retention time.
Warning: Feature 1193 looks odd for at least one peak. Please check afterwards.
Warning: Feature 1190 looks odd for at least one peak. Please check afterwards.
Warning: Feature 239 looks odd for at least one peak. Please check afterwards.
Warning: Feature 1195 looks odd for at least one peak. Please check afterwards.
Warning: Feature 1204 looks odd for at least one peak. Please check afterwards.
Warning: Feature 236 looks odd for at least one peak. Please check afterwards.
Warning: Feature 10783 looks odd for at least one peak. Please check afterwards.
Warning: Feature 6130 looks odd for at least one peak. Please check afterwards.
Warning: Feature 10777 looks odd for at least one peak. Please check afterwards.
Warning: Feature 10790 looks odd for at least one peak. Please check afterwards.
Warning: Feature 1666 looks odd for at least one peak. Please check afterwards.
Warning: Feature 1672 looks odd for at least one peak. Please check afterwards.
Warning: Feature 3679 looks odd for at least one peak. Please check afterwards.
Warning: Feature 10786 looks odd for at least one peak. Please check afterwards.
Warning: Feature 4177 looks odd for at least one peak. Please check afterwards.
Warning: Feature 4185 looks odd for at least one peak. Please check afterwards.
Warning: Feature 1207 looks odd for at least one peak. Please check afterwards.
Warning: Feature 6139 looks odd for at least one peak. Please check afterwards.
....
*ect Ive cut the warnings down to save space. There were 623, same as the amount of samples*
Created 796 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 34751
Start grouping after correlation.
Generating EIC's ..
Warning: Found NA peaks in selected sample.
Calculating peak correlations in 796 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating isotope assignments in 796 Groups...
% finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 796 Groups...
% finished: 10
The function has been hanging here for about a day.
I have two questions:
One, what do these warnings imply? I haven't received it before. I looked into the CAMERA source code to try and clarify but I am still not sure what it is implying.
Two, is there an obvious reason my code would be hanging here? I have run CAMERA a lot and never experienced it hanging like this before.
Thanks for any insights you all might have. If there is any more info I should provided or other places I should inquire let me know.
Thanks
Henry Holm
PhD Student