"obsNames" in argsCorrNetwork argument missing. Not performing correlation network calculation.

[ThomasPouplin]

I'm a new compMS2Miner user. Although I managed to go through the demo dataset and script without any issue, that's a different outcome when trying with my own data.

I'm running the script on a reduced dataset. 2 groups with 5 replicates in each. I generated a peaktable "MS1features" (from METMSLine actually) with molecular features as rows and samples in columns (with the first 3 columns being EIC# (=molecular features), mz and RT.

My obsNames are: [1] "Coli_01" "Coli_02" "Coli_03" "Coli_04" "Coli_05" "Typhi_01" "Typhi_02" "Typhi_03" "Typhi_04" "Typhi_05"

I have 10 mzXML files (5 Coli, 5 Typhi - matching the obsNames) generated from wiff files using proteowizrd with a peakpicking level 1 to 2 (to get MS2).

However, when trying to construct the compMS2 : compMS2Demo <- compMS2Construct(MS1features = peakTable, msDataDir = mzXmlDir_example, nCores=nCores, mode = "neg", precursorPpm = 10, ret = 20, TICfilter = 500)

It starts the process:

"creating compMS2 object in positive ionisation mode 10 MS2 (.mzXML) file(s) were detected within the directory... Starting SNOW cluster with 4 local sockets... matching MS1 peak table features to the following MS2 files: Coli_01.mzXML Coli_02.mzXML Coli_03.mzXML Coli_04.mzXML Coli_05.mzXML CTRL_01.mzXML CTRL_02.mzXML CTRL_03.mzXML CTRL_04.mzXML CTRL_05.mzXML 1 of 10 complete (Coli_01.mzXML). 2 of 10 complete (Coli_02.mzXML). 3 of 10 complete (Coli_03.mzXML). 4 of 10 complete (Coli_04.mzXML). 5 of 10 complete (Coli_05.mzXML). 6 of 10 complete (CTRL_01.mzXML). 7 of 10 complete (CTRL_02.mzXML). 8 of 10 complete (CTRL_03.mzXML). 9 of 10 complete (CTRL_04.mzXML). 10 of 10 complete (CTRL_05.mzXML).

But then fails with the following message:

"obsNames" in argsCorrNetwork argument missing. Not performing correlation network calculation.

I tried with adding the argument "argsCorrNetwork = obsNames" to the compMSConstruct function but here with this message: Error: $ operator is invalid for atomic vectors

I couldn't go any further as it locks the rest of the script - compMS2demo not being created.

Any clue to share ?

Thanks !!!

Thomas

SessionInfo()

R version 3.4.1 (2017-06-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

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

other attached packages: [1] doParallel_1.0.10 DT_0.2 scales_0.5.0 rhandsontable_0.3.4 igraph_1.1.2 shiny_1.0.5
[7] doSNOW_1.0.14 snow_0.4-2 iterators_1.0.8 foreach_1.4.3 compMS2Miner_2.3.0

loaded via a namespace (and not attached): [1] Rcpp_0.12.12 plyr_1.8.4 compiler_3.4.1 nloptr_1.0.4 git2r_0.19.0 tools_3.4.1
[7] digest_0.6.12 lme4_1.1-13 jsonlite_1.5 memoise_1.1.0 nlme_3.1-131 lattice_0.20-35
[13] pkgconfig_2.0.1 Matrix_1.2-11 yaml_2.1.14 curl_2.8.1 withr_2.0.0 httr_1.3.1
[19] htmlwidgets_0.9 MatrixModels_0.4-1 devtools_1.13.3 stats4_3.4.1 grid_3.4.1 R6_2.2.2
[25] minqa_1.2.4 magrittr_1.5 codetools_0.2-15 htmltools_0.3.6 MASS_7.3-47 splines_3.4.1
[31] mime_0.5 colorspace_1.3-2 xtable_1.8-2 httpuv_1.3.5 munsell_0.4.3