Ideom, Is it possible to change xcmsSet method?

Adewale — Fri, 29 Jul 2016 15:51:54 -0000

Probably not possible. I think the whole mzmatch plus ideom ormetassign was built for centwave. Just saw that on their website

Ideom, Is it possible to change xcmsSet method?

Adewale — Fri, 29 Jul 2016 15:25:21 -0000

I get this warning that my files may be in profile mode rather than centroid, so centwave won't work. This is when runnig the second macro in Ideom. Because a peakml file was still generated, I attempted to continue, but more errors come downstream.

How to change XcmsSet method in Ideom from centwave to others

Adewale — Fri, 29 Jul 2016 15:12:51 -0000

Gap filling error while running mzmatch

Jagajjit Sahu — Mon, 04 Jul 2016 11:39:16 -0000

Hi All. I had successfully run the mzmatch codes on the tutorial data but suddenly it started prompting this error. Can anybody help me please?

While running-
PeakML.GapFiller(filename = "final_combined_blank_filtered.peakml", ionisation = "detect", outputfile = "final_combined_gapfilled.peakml", ppm = 0, rtwin = 0, fillAll=TRUE,Rawpath=NULL)

getting the error-

Error in unsafeFindInterval3(c(mz_start, mz_finis), massData) :
4 arguments passed to .Internal(findInterval) which requires 5
Error in unsafeFindInterval3(c(mz_start, mz_finis), massData) :
4 arguments passed to .Internal(findInterval) which requires 5
Error in unsafeFindInterval3(c(mz_start, mz_finis), massData) :
4 arguments passed to .Internal(findInterval) which requires 5
Error in unsafeFindInterval3(c(mz_start, mz_finis), massData) :
......

problems running mzmatch

Adewale — Fri, 20 May 2016 06:00:53 -0000

Hi, all. pls help.
I am having problems with sourceforge and R connection. I am trying to use mzmatch as part of my workflow on R. I have already installed mzmatch.R After loading the library mzmatch.R, When I call 'mzmatch.init()' R tries to download dbs but cannot. Here below is the error:

mzmatch.init()
trying URL 'http://sourceforge.net/projects/mzmatch/files/mzmatch.R/dbs.zip/download'
Error in download.file("http://sourceforge.net/projects/mzmatch/files/mzmatch.R/dbs.zip/download", :
cannot open URL 'http://sourceforge.net/projects/mzmatch/files/mzmatch.R/dbs.zip/download'

(a) Internet connections are working, as I have used R to get all other packages at the same time as this.
I have changed repositories (below)over and over again, none of them works.
Besides sourceforge is not in my repositories and R Forge does not work for the 'dbs'

setRepositories()
--- Please select repositories for use in this session ---

1: + CRAN 2: BioC software
3: BioC annotation 4: BioC experiment
5: BioC extra 6: + CRAN (extras)
7: Omegahat 8: R-Forge
9: rforge.net 10: CRAN (extras, https)
11: R-Forge [https] 12: rforge.net [https]

I use R 3.2.5

sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

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

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

other attached packages:
[1] mzmatch.R_2.0-13 xcms_1.46.0 Biobase_2.30.0
[4] ProtGenerics_1.2.1 BiocGenerics_0.16.1 mzR_2.4.1
[7] Rcpp_0.12.4

loaded via a namespace (and not attached):
[1] lattice_0.20-33 ptw_1.9-11 tcltk_3.2.5
[4] caTools_1.17.1 tools_3.2.5 grid_3.2.5
[7] R.oo_1.18.2 snow_0.4-1 KernSmooth_2.23-15
[10] gtools_3.5.0 rJava_0.9-8 RColorBrewer_1.1-2
[13] nloptr_1.0.4 R.utils_1.32.5 bitops_1.0-6
[16] codetools_0.2-14 gdata_2.17.0 gplots_3.0.1
[19] R.methodsS3_1.6.2 XML_3.98-1.4

(b) Manually downloading the file from source forge and installing in R does not work as R does not load because description, namespace, index, md5,news files are missing.
(c) using 'download.file' function does not work also
Thanks

How to deal with 2 columns

Cara Green — Thu, 29 Oct 2015 09:16:49 -0000

I can get mzmatch to work fine but I was wondering the best way to deal with an analysis using two columns (c18 and anion exchange). Is the best way just to run the whole analysis twice with each column. I'm guessing the peaks would be too different for the same metabolite to be able to combine the data into one analysis.
Thanks,

Cara

help with centWave

Adriana Cabanela — Mon, 13 Jul 2015 19:26:35 -0000

Hello, I'm using for the first time and I'm finding the error above. How can I fix it?

library(mzmatch.R)
Carregando pacotes exigidos: Rcpp
Carregando pacotes exigidos: xcms
Carregando pacotes exigidos: mzR
Carregando pacotes exigidos: BiocGenerics
Carregando pacotes exigidos: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit

Carregando pacotes exigidos: ProtGenerics
Carregando pacotes exigidos: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: ‘xcms’

The following objects are masked from ‘package:Biobase’:

phenoData, phenoData<-

mzmatch.init(version.1=FALSE)
C:/Program Files/R/R-3.2.1/library/mzmatch.R/java/mzmatch_2.0.jar

mzmatch.R.Setup(samplelist="sample_setup.tsv")

xseto <- xcmsSet(sampleList$filenames, method='centWave', ppm=2,
+ peakwidth=c(10,100), snthresh=5, prefilter=c(3,1000),
+ integrate=1, mzdiff=0.01, verbose.columns=TRUE,
+ fitgauss=FALSE, nSlaves=4)

Attaching package: ‘snow’

The following objects are masked from ‘package:BiocGenerics’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, parApply, parCapply,
parLapply, parRapply, parSapply

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
parCapply, parLapply, parRapply, parSapply, splitIndices,
stopCluster

Starting snow cluster with 4 local sockets.
Detecting features in file # 1 : 1_LIT_01_Pos_000001.mzML
Detecting features in file # 2 : 1_LIT_02_Pos_000001.mzML
Detecting features in file # 3 : 2_Tau_01_Pos_000001.mzML
Detecting features in file # 4 : 2_Tau_02_Pos_000001.mzML
Detecting features in file # 5 : 3_PAF_01_Pos_000001.mzML
Detecting features in file # 6 : 3_PAF_02_Pos_000001.mzML
Detecting features in file # 7 : 4_PAF_SR_01_Pos_000001.mzML
Detecting features in file # 8 : 4_PAF_SR_02_Pos_000001.mzML
Detecting features in file # 9 : 5_TAU_LPC_01_Pos_000001.mzML
Detecting features in file # 10 : 5_TAU_LPC_02_Pos_000001.mzML
Detecting features in file # 11 : 6_TAU_LPC_SR_01_Pos_000001.mzML
Detecting features in file # 12 : 6_TAU_LPC_SR_02_Pos_000001.mzML
Error in checkForRemoteErrors(val) :
12 nodes produced errors; first error: 'from' deve ter comprimento 1

problems with install

Adriana Cabanela — Wed, 08 Jul 2015 19:04:42 -0000

I finally realized that the R.utils was missing and if I tried to install it, might work. And it did. I manage to finish the install.
In case anyone new in using R have the same problem, this is how to fix it:

install.packages (c("R.utils"))

source ("http://puma.ibls.gla.ac.uk/mzmatch.R/install_mzmatch.R")

Sorry for the kind of dumb question.

problems with install

Adriana Cabanela — Wed, 08 Jul 2015 17:01:28 -0000

Hello, I'm new to this program. I'm trying to install it, but I receive the following message. How could I solve this?
Thanks in advance,
Adriana

source ("http://puma.ibls.gla.ac.uk/mzmatch.R/install_mzmatch.R")
tentando a URL 'http://puma.ibls.gla.ac.uk/mzmatch.R/mzmatch.R.tar.gz'
Content type 'application/x-gzip' length 118159 bytes (115 KB)
downloaded 115 KB

ERROR: dependency 'R.utils' is not available for package 'mzmatch.R'
* removing 'C:/Program Files/R/R-3.2.1/library/mzmatch.R'
Warning messages:
1: execução do comando '"C:/PROGRA~1/R/R-32~1.1/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.2.1\library" "mzmatch.R.tar.gz"' teve status 1
2: In install.packages(pkgs = "mzmatch.R.tar.gz", repos = NULL, type = "source") :
installation of package ‘mzmatch.R.tar.gz’ had non-zero exit status

Recent posts to Discussion

Ideom, Is it possible to change xcmsSet method?

Ideom, Is it possible to change xcmsSet method?

How to change XcmsSet method in Ideom from centwave to others

Gap filling error while running mzmatch

problems running mzmatch

How to deal with 2 columns

help with centWave

problems with install

problems with install