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Messages - edmandsw

1
XCMS / Re: sequential addition of files to an xcms object
You might be interested in an R package simExTargId I have been developing for real-time metabolomic experiment monitoring (with email notification) and MS/MS target identification. It makes use of xcms and CAMERA and sequentially concatenates xcmsSet objects as data is collected. It is still in development and has a few rough edges but it has been used regularly in our lab (it currently works for Agilent .d and Thermo .raw/.RAW data files).
2
XCMS / Re: sequential addition of files to an xcms object
As far as I'm aware this isn't possible. The retention time correction using the obiwarp method for example has to be reassessed with a new centre sample.
See the help file
Code: [Select]
?retcor.obiwarp
#center	
#the index of the sample all others will be aligned to. If center==NULL, the sample with the most peaks is chosen as default
So the retention time deviation for each file has to be re-calculated.
Additionally for grouping the minfrac and minsamp arguments will be affected by additional samples in each group as you concatenate.
Code: [Select]
?group.density
#minfrac	
#minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group
#minsamp	
#minimum number of samples necessary in at least one of the sample groups for it to be a valid group

It shouldn't be (computationally speaking) too much of a big deal to re-do the retention time correction and grouping each time you peak-pick an additional file(s). The most time-consuming part is definitely the xcmsSet function.
3
XCMS / Re: No console messages xcmsSet (xcms v1.50.1)
Fantastic, thanks for getting back to me so quickly. I read Martin Morgan's explanation also and it is now clear to me (although probably quite superficially)  how BiocParallel is working.   :))
4
XCMS / No console messages xcmsSet (xcms v1.50.1)
Hi,

It is probably something minor/trivial but since updating to xcms3 (v1.50.1) (and the deprecation of the nSlaves argument change to BPPARAM of BiocParallel) I am no longer receiving lovely reassuring progress messages printed to the R console. The strange thing is in previous versions of xcms the progress messages would appear soon after initiation of the xcmsSet function regardless of the number of mzXML files in the directory.
I have tried the progressBar argument of the SnowParam function but it was stuck at 0% for over an hour.
With the ~200 mzXML files I am currently peak-picking I did not receive any console message for over two hours:
metabForum_20170608.PNG
Then all of a sudden there were messages previously typical of a single-threaded process:
metabForum_20170608_2.PNG
However I was able to check the multi-threaded process was running by monitoring the CPU usage.

When the dataset size is small as is the case for faahKO, the progress messages appear much sooner. Here is a reproducible but perhaps not very useful example:
Code: [Select]
library(faahKO)
library(xcms)
library(BiocParallel)
library(snow)

## The directory with the NetCDF LC/MS files
cdfpath <- file.path(find.package("faahKO"), "cdf")

setwd(cdfpath)

snowparam <- SnowParam(workers = parallel::detectCores(), type = "SOCK")

peakmatrix <- xcmsSet(BPPARAM = snowparam)

Is is necessary to DIY/Jerry-rig your own progressCallBack function now?

Code: [Select]
cdffiles <- list.files(cdfpath, recursive = TRUE)
progress <- function(n) cat(paste0(n, ' of ', length(cdffiles),
                                   ' complete (', basename(cdffiles)[n],
                                   ').\n'))
peakmatrix <- xcmsSet(BPPARAM = snowparam, progressCallback = progress)
Although this didn't work as expected either.

Many thanks in advance,

Will

Code: [Select]
>sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats    graphics  grDevices utils    datasets  methods  base    

other attached packages:
[1] snow_0.4-2          BiocParallel_1.8.1  faahKO_1.14.0      xcms_1.50.1        Biobase_2.34.0    
[6] ProtGenerics_1.6.0  BiocGenerics_0.20.0 mzR_2.8.1          Rcpp_0.12.10      

loaded via a namespace (and not attached):
[1] RANN_2.5              lattice_0.20-34        codetools_0.2-15      MASS_7.3-45          
[5] MassSpecWavelet_1.40.0 grid_3.3.2            plyr_1.8.4            stats4_3.3.2          
[9] S4Vectors_0.12.1      Matrix_1.2-8          splines_3.3.2          RColorBrewer_1.1-2    
[13] tools_3.3.2            survival_2.40-1        multtest_2.30.0     

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