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errors meet in example 6.12 in page 162 in the Supplementary Text and Figures of paper "A multicenter study benchmarks software tools for label-free proteome quantification" #7

Closed little-jun closed 4 years ago

little-jun commented 4 years ago

when i execute the example 6.12 in page 162 in the Supplementary Text and Figures of your paper "A multicenter study benchmarks software tools for label-free proteome quantification", when i run the code : nix = sapply( inputFiles, FSWE.generateReports, softwareSource = "guess", keep_original_names = T, singleHits = F, plotHistogram = T, plotHistNAs = T, reportSequences = F ) i meet errors "Error in guessSoftwareSource(experimentFile, FSWE.softwareNames) : Software source can not be guessed by filename! Review file names: they should start by the software source!File: LFQbench.R" Can you explain the reason for me , thank you .

mesontau commented 4 years ago

Hi, could you please provide your input files? Thanks, Pedro Navarro.

little-jun commented 4 years ago

Hi, could you please provide your input files? Thanks, Pedro Navarro.

i have solved the error, but i meet a new error. my input file is in the folder \ext\data\vignette_examples\hye124

my code is `## ----include=FALSE-------------------------------------------------------

define here global settings

knitr::opts_chunk$set(echo=TRUE, warning=FALSE, message=FALSE, results="hide", fig.width = 7, fig.height = 5)

----defineSampleSetComosition-------------------------------------------

sampleComposition = data.frame( species = c("HUMAN","YEAST", "ECOLI"), A = c( 67, 30, 3 ), B = c( 67, 3, 30 ) )

----defineDatasets------------------------------------------------------

dataSets = data.frame( "HYE110_SynaptG2S" = c( paste(rep("HYE110_A"), 1:3, sep = "."), paste(rep("HYE110_B"), 1:3, sep = ".") ), row.names = c( "A1", "A2", "A3", "B1", "B2", "B3" ) )

----defineSpeciesTags---------------------------------------------------

speciesTags = list( HUMAN = "_HUMAN", YEAST = "_YEAS", ECOLI = "_ECOLI" )

----initLFQbench--------------------------------------------------------

library(LFQbench)

LFQbench.initConfiguration( SampleComposition = sampleComposition )

FSWE.initConfiguration( injectionNames = dataSets, speciesTags = speciesTags )

----sourceDir-----------------------------------------------------------

srcDir = "D:/LFQbench/LFQbench-master/ext/data/vignette_examples/hye110"

LFQbench.setDataRootFolder( rootFolder = srcDir, createSubfolders = T )

----listSoftwareConfig, results="asis"----------------------------------

print( paste( FSWE.softwareNames, collapse="," ) )

----addSoftwareConfig---------------------------------------------------

FSWE.addSoftwareConfiguration(

Software configuration name

softwareName = "ISOQuant_pep",

# input_format can be wide or long. 
# Wide contains all quantitative values (all samples and replicates) 
# for a peptide in a single row, 
# whereas long contains a single quantitative value (just one replicate) in a row.
input_format = "wide",

# it is important to know that LFQbench honours the extension: 
# csv are COMMA separated values, 
# tsv are TAB separated values
input.extension = "*.csv$",

# how NA (not available) values are reported
nastrings = " ",

# in long formats, how the quantitative value column is named
quantitative.var = make.names("intensity in"),

# in wide formats, how quantitative values are tagged 
#(they also should include the injection names reported at the datasets object)
quantitative.var.tag = make.names("intensity in"),

# name of the protein name variable. 
# Remember: protein names should include species information (speciesTags)
protein.var = "entry",

# variable name of sequence 
# (including modifications as defined in FSWE.modificationsToUniMod)
sequence.mod.var = "sequence",

# variable name of the precursar charge state.
charge.var = make.names("signal_charge")

)

----addModification-----------------------------------------------------

FSWE.addModification( modificationRegExps = "\[Oxi\]", UniModStrings = "\(UniMod:35\)" )

list modifications available

print( FSWE.modificationsToUniMod )

----Generate reports in LFQbench format----------------------------------

inputFiles=list.files( path=LFQbench.Config$DataRootFolder, pattern="\..+" ) nix = sapply( inputFiles, FSWE.generateReports, softwareSource = "guess", keep_original_names = T, singleHits = F, plotHistogram = T, plotHistNAs = T, reportSequences = F )

----Perform LFQbench analysis----------------------------------------------

some configuration changes for beautifying plots

LFQbench.changeConfiguration( LogIntensityPlotRange = c( 9,21), LogRatioPlotRange = c(-7,7) )

run batch analysis and keep resultset

res = LFQbench.batchProcessRootFolder( )

----Display metrics---------------------------------------------

getting the result set of the first benchmarked file

rs = res[[1]] m = LFQbench.getMetrics( resultSet = rs )

get local accuracy and precision(byintensitytertiles)

acc = m$Local accuracy$A:B prec = m$Local precision$A:B

----Display plots---------------------------------------------

get the benchmark result for the first sample pair of the recently used result set

samplePairRes = rs$result[[1]]

display the scatter plot

LFQbench.showScatterAndBoxPlot( samplePair = samplePairRes, showLegend = T )

display the distributions of log ratios

LFQbench.showDistributionDensityPlot( samplePair = samplePairRes , showLegend = F )

----defineSampleSetComosition-------------------------------------------

sampleComposition = data.frame( species = c("HUMAN","YEAST", "ECOLI"), A = c( 65, 30, 05 ), B = c( 65, 15, 20 ) )

----defineDatasets------------------------------------------------------

dataSets = data.frame( "HYE124_TTOF6600_64var" = c( " lgillet_I150211_008", "lgillet_I150211_010", "lgillet_I150211_012", ## A " lgillet_I150211_009", "lgillet_I150211_011", "lgillet_I150211_013 " ## B ) , row.names = c ( "A1" , "A2" , "A3" , "B1" , "B2" , "B3" ) )

----defineSpeciesTags---------------------------------------------------

speciesTags = list( HUMAN = "_HUMAN", YEAST = "_YEAS", ECOLI = "_ECOLI" )

LFQbench.initConfiguration( SampleComposition = sampleComposition )

FSWE.initConfiguration( injectionNames = dataSets, speciesTags = speciesTags )

we don't need to define new software report format in this example

because Spect ronaut and PeakView (SWATH 2.0) report formats are predefined in FSWE

----sourceDir-----------------------------------------------------------

srcDir = "D:/LFQbench/LFQbench-master/ext/data/vignette_examples/hye124"

LFQbench.setDataRootFolder( rootFolder = srcDir, createSubfolders = T )

inputFiles=list.files( path=LFQbench.Config$DataRootFolder, pattern="\..+" )

nix = sapply( inputFiles, FSWE.generateReports, softwareSource = "guess", keep_original_names = T, singleHits = F, plotHistogram = T, plotHistNAs = T, reportSequences = F )

hye124.res = LFQbench.batchProcessRootFolder( )`

the error is "Can't use numeric NA as column index with [." when i execute the code in the last. `nix = sapply( inputFiles, FSWE.generateReports, softwareSource = "guess", keep_original_names = T, singleHits = F, plotHistogram = T, plotHistNAs = T, reportSequences = F )'

the correct error is "错误: Can't use numeric NA as column index with [. Run rlang::last_error() to see where the error occurred.

rlang::last_error() <error/rlang_error> Can't use numeric NA as column index with [. Backtrace:

  1. base::source(...)
  2. base::sapply(...) LFQbench-master/vignettes/LFQbench.R:52:0
  3. base::lapply(X = X, FUN = FUN, ...)
  4. LFQbench:::FUN(X[[i]], ...)
  5. tibble:::[.tbl_df(peptides_wide, , c(c(1:3), experiment.order))
  6. tibble:::check_names_df(j, x)
  7. tibble:::check_names_df_numeric(j, x) Run rlang::last_trace() to see the full context. rlang::last_trace() <error/rlang_error> Can't use numeric NA as column index with [. Backtrace: x
  8. +-base::source(...)
  9. | +-base::withVisible(eval(ei, envir))
  10. | -base::eval(ei, envir)
  11. | -base::eval(ei, envir)
  12. -base::sapply(...) LFQbench-master/vignettes/LFQbench.R:52:0
  13. -base::lapply(X = X, FUN = FUN, ...)
  14. -LFQbench:::FUN(X[[i]], ...)
  15. +-peptides_wide[, c(c(1:3), experiment.order)]
  16. +-dplyr:::[.grouped_df(peptides_wide, , c(c(1:3), experiment.order))
  17. +-base::NextMethod()
  18. -tibble:::[.tbl_df(peptides_wide, , c(c(1:3), experiment.order))
  19. -tibble:::check_names_df(j, x)
  20. -tibble:::check_names_df_numeric(j, x)"
mesontau commented 4 years ago

my input file is in the folder \ext\data\vignette_examples\hye124

In that folder there is not any file related to a Synapt G2S, as your code suggests:

 dataSets = data.frame(
 "HYE110_SynaptG2S" = c(
 paste(rep("HYE110_A"), 1:3, sep = "."),
 paste(rep("HYE110_B"), 1:3, sep = ".")
 ),

Also later in your code you change your source directory:

srcDir = "D:/LFQbench/LFQbench-master/ext/data/vignette_examples/hye110"

And later again you change the datasets:

dataSets = data.frame(
"HYE124_TTOF6600_64var" = c(
" lgillet_I150211_008", "lgillet_I150211_010", "lgillet_I150211_012", ## A
" lgillet_I150211_009", "lgillet_I150211_011", "lgillet_I150211_013 " ## B
) ,
row.names = c ( "A1" , "A2" , "A3" , "B1" , "B2" , "B3" )
)

Could you please clarify your code? It is hard to know what data you are trying to analyse.

Thanks, Pedro Navarro.