Filtervariable

PB_2023 · June 14, 2023, 6:00am

Hello,
I got following error while trying to do analysis in metaboanalsytR.

rawData ← ImportRawMSData(NULL, tar_path, plotSettings = SetPlotParam(Plot=FALSE))
Not a real initialized mSet found, will re-initialize one automatically !

Step 2/6: Start to import the spectrum!
This step will take a short time…
Raw file import begin…
Step 2/6: Successfully imported raw MS data! (2023-06-13 23:28:46.081761)
Going to the next step…
Warning message:
In ImportRawMSData(NULL, tar_path, plotSettings = SetPlotParam(Plot = FALSE)) :
No metadata provided, all files in one sub-folder will be considered a group!

rawData ← ImportRawMSData(NULL, metaboanalyst_input.csv, plotSettings = SetPlotParam(Plot=FALSE))
Not a real initialized mSet found, will re-initialize one automatically !
Error: object ‘metaboanalyst_input.csv’ not found
rawData ← ImportRawMSData(NULL, “metaboanalyst_input.csv”, plotSettings = SetPlotParam(Plot=FALSE))
Not a real initialized mSet found, will re-initialize one automatically !

ERROR: No standard MS file found ! Please check the extension of your data.
Error in ImportRawMSData(NULL, “metaboanalyst_input.csv”, plotSettings = SetPlotParam(Plot = FALSE)) :

In addition: Warning message:
In Path2Files(path = path) :
Wrong file format detected, Only mzML, mzXML, mzData or CDF will be included.

rawData ← ImportRawMSData(NULL,tar_path, plotSettings = SetPlotParam(Plot=FALSE))
Not a real initialized mSet found, will re-initialize one automatically !

Step 1/6: Start to import the spectrum!
This step will take a short time…
Raw file import begin…
Step 1/6: Successfully imported raw MS data! (2023-06-13 23:32:01.835412)
Going to the next step…
Warning message:
In ImportRawMSData(NULL, tar_path, plotSettings = SetPlotParam(Plot = FALSE)) :
No metadata provided, all files in one sub-folder will be considered a group!

mSet ← PerformPeakProfiling(rawData,param_optimized$best_parameters,

                         plotSettings = SetPlotParam(Plot = T))

6 CPU Threads will be used for peak profiling !

Step 3/6: Started peak picking! This step will take some time…
Warning messages:
1: In PerformPeakProfiling(rawData, param_optimized$best_parameters, :
Param is missing. Will use the default generic/general params,
but optimization with PerformParamsOptimization is strongly recommanded !
2: In doTryCatch(return(expr), name, parentenv, handler) :
display list redraw incomplete
3: In doTryCatch(return(expr), name, parentenv, handler) :
invalid graphics state
4: In doTryCatch(return(expr), name, parentenv, handler) :
invalid graphics state

rawData ← ImportRawMSData(NULL,raw_data, plotSettings = SetPlotParam(Plot=FALSE))
Not a real initialized mSet found, will re-initialize one automatically !
Error in path.expand(path) : invalid ‘path’ argument
rawData ← ImportRawMSData(NULL,“~/raw_data”, plotSettings = SetPlotParam(Plot=FALSE))
Not a real initialized mSet found, will re-initialize one automatically !
Error in Path2Files(path = path) : Invalid path provided, please check!
In addition: Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
display list redraw incomplete
2: In doTryCatch(return(expr), name, parentenv, handler) :
invalid graphics state
3: In doTryCatch(return(expr), name, parentenv, handler) :
invalid graphics state
4: In doTryCatch(return(expr), name, parentenv, handler) :
display list redraw incomplete
5: In doTryCatch(return(expr), name, parentenv, handler) :
invalid graphics state
6: In doTryCatch(return(expr), name, parentenv, handler) :
invalid graphics state
7: In normalizePath(path) :
path[1]=“/Users/prabinadhiren/raw_data”: No such file or directory
rawData ← ImportRawMSData(NULL,raw_data, plotSettings = SetPlotParam(Plot=FALSE))
Not a real initialized mSet found, will re-initialize one automatically !
Error in path.expand(path) : invalid ‘path’ argument
rawData ← ImportRawMSData(NULL,“raw_data”, plotSettings = SetPlotParam(Plot=FALSE))
Not a real initialized mSet found, will re-initialize one automatically !
Error in Path2Files(path = path) : Invalid path provided, please check!
In addition: Warning message:
In normalizePath(path) : path[1]=“raw_data”: No such file or directory
rawData ← ImportRawMSData(NULL,tar_path, plotSettings = SetPlotParam(Plot=FALSE))
Not a real initialized mSet found, will re-initialize one automatically !

Step 1/6: Start to import the spectrum!
This step will take a short time…
Raw file import begin…
Step 1/6: Successfully imported raw MS data! (2023-06-13 23:36:27.280722)
Going to the next step…
Warning message:
In ImportRawMSData(NULL, tar_path, plotSettings = SetPlotParam(Plot = FALSE)) :
No metadata provided, all files in one sub-folder will be considered a group!

mSet ← PerformPeakProfiling(rawData,param_optimized$best_parameters,

                         plotSettings = SetPlotParam(Plot = T))

6 CPU Threads will be used for peak profiling !

Step 3/6: Started peak picking! This step will take some time…
ROI searching under 5 ppm … Detecting peaks in 239314 regions of interest of 1a.mzML … OK: 16267 found.

ROI searching under 5 ppm … Detecting peaks in 274940 regions of interest of 3a.mzML … OK: 15289 found.

ROI searching under 5 ppm … Detecting peaks in 313501 regions of interest of 2a.mzML … OK: 17757 found.

Step 3/6: Peak picking finished ! (2023-06-13 23:41:32.997367)

Step 4/6: Started peak alignment! This step is running…
Total of 12795 slices detected for processing… Done !
Going to the next step…
No blank sample included based on grouping info. Skipped!
PeakGroup – loess is used for retention time correction…
Performing retention time correction using 4561 peak groups.
Applying retention time adjustment to the identified chromatographic peaks … Done !
Total of 12795 slices detected for processing… Done !
Going to the next step…
Step 4/6: Peak alignment finished ! (2023-06-13 23:42:00.036178)

Step 5/6: Started peak filling! This step may take some time…
Starting peak filling!
Defining peak areas for filling-in…
No missing peaks present.
Step 5/6: Peak filing finished ! (2023-06-13 23:42:00.995636)
Peak Profiling finished successfully !
Begin to plotting figures…Done !
Warning message:
In PerformPeakProfiling(rawData, param_optimized$best_parameters, :
Param is missing. Will use the default generic/general params,
but optimization with PerformParamsOptimization is strongly recommanded !

annParams ← SetAnnotationParam(polarity = “negative”, mz_abs_add = 0.005)
annotPeaks ← PerformPeakAnnotation(mSet, annParams)

Step 6/6: Starting Peak Annotation…
Start grouping after retention time.
Created 470 pseudospectra.
Generating peak matrix…
Run isotope peak annotation…
Found isotopes:1532
Start grouping after correlation…
Generating EIC’s…
Detecting 1a.mzML … 2972 peaks found!
Detecting 2a.mzML … 2569 peaks found!
Detecting 3a.mzML … 1615 peaks found!
Calculating peak correlations in 470 Groups…
Calculating graph cross linking in 470 Groups…
New number of ps-groups: 3198
mSet has now 3198 groups, instead of 470 !
Generating peak matrix for peak annotation!
Polarity is set in annotaParam: negative
Ruleset could not read from object! Recalculating…
Calculating possible adducts in 3198 Groups…
Step 6/6: Successfully performed peak annotation! (2023-06-13 23:44:32.937348)
Going to the final step…

maPeaks ← FormatPeakList(annotPeaks, annParams, filtIso =F, filtAdducts = FALSE, missPercent = 1)
write.csv(maPeaks@dataSet, file = “metaboanalyst_input.csv”,row.names = F)
mSet<-InitDataObjects(“pktable”, “stat”, FALSE)
mSet<-Read.TextData(mSet, “metaboanalyst_input.csv”, “colu”, “disc”)
Error in Read.TextData(mSet, “metaboanalyst_input.csv”, “colu”, “disc”) :
object ‘“disc”’ not found
mSet<-Read.TextData(mSet, “metaboanalyst_input.csv”, “colu”)
Error in Read.TextData(mSet, “metaboanalyst_input.csv”, “colu”) :
object ‘“colu”’ not found
mSet<-Read.TextData(mSet, “metaboanalyst_input.csv”)
Error in Read.TextData(mSet, “metaboanalyst_input.csv”) :
object ‘“metaboanalyst_input.csv”’ not found

Read the text data into the mSet object

anal.type ← “regression”

Read text data into an mSet object

mSet ← Read.TextData(file = “metaboanalyst_input.csv”)
Error in *tmp*$dataSet : $ operator is invalid for atomic vectors

Access the data within the mSet object

data ← exprs(mSet) # or assay(mSet)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘exprs’ for signature ‘“NULL”’
write.csv(maPeaks@dataSet, file = “metaboanalyst_input.csv”,row.names = F)
mSet<-InitDataObjects(“pktable”, “stat”, FALSE)
mSet<-Read.TextData(mSet, “metaboanalyst_input.csv”)
Error in if (mSetObj$dataSet$paired) { : argument is of length zero
write.csv(maPeaks@dataSet, file = “metaboanalyst_input.csv”,row.names = F)
mSet<-Read.TextData(mSet, “metaboanalyst_input.csv”)
Error in if (mSetObj$dataSet$paired) { : argument is of length zero
mSet<-Read.TextData(mSet1, “metaboanalyst_input.csv”)
Error: object ‘mSet1’ not found
mSet1 ← FormatPeakList(mSet = mSet, annParams, filtIso =F, filtAdducts = FALSE,missPercent = 1)
Error in mSet@WorkingDir :
no applicable method for @ applied to an object of class “NULL”
mSet ← PerformPeakProfiling(rawData,param_optimized$best_parameters,

                         plotSettings = SetPlotParam(Plot = T))

6 CPU Threads will be used for peak profiling !

Step 3/6: Started peak picking! This step will take some time…
ROI searching under 5 ppm … Detecting peaks in 274940 regions of interest of 3a.mzML … OK: 15289 found.

ROI searching under 5 ppm … Detecting peaks in 239314 regions of interest of 1a.mzML … OK: 16267 found.

ROI searching under 5 ppm … Detecting peaks in 313501 regions of interest of 2a.mzML … OK: 17757 found.

Step 3/6: Peak picking finished ! (2023-06-13 23:52:48.205892)

Step 4/6: Started peak alignment! This step is running…
Total of 12795 slices detected for processing… Done !
Going to the next step…
No blank sample included based on grouping info. Skipped!
PeakGroup – loess is used for retention time correction…
Performing retention time correction using 4561 peak groups.
Applying retention time adjustment to the identified chromatographic peaks … Done !
Total of 12795 slices detected for processing… Done !
Going to the next step…
Step 4/6: Peak alignment finished ! (2023-06-13 23:53:16.086768)

Step 5/6: Started peak filling! This step may take some time…
Starting peak filling!
Defining peak areas for filling-in…
No missing peaks present.
Step 5/6: Peak filing finished ! (2023-06-13 23:53:17.112173)
Peak Profiling finished successfully !
Begin to plotting figures…Done !
Warning message:
In PerformPeakProfiling(rawData, param_optimized$best_parameters, :
Param is missing. Will use the default generic/general params,
but optimization with PerformParamsOptimization is strongly recommanded !

annParams ← SetAnnotationParam(polarity = “negative”, mz_abs_add = 0.005)
annotPeaks ← PerformPeakAnnotation(mSet, annParams)

Step 6/6: Starting Peak Annotation…
Start grouping after retention time.
Created 470 pseudospectra.
Generating peak matrix…
Run isotope peak annotation…
Found isotopes:1532
Start grouping after correlation…
Generating EIC’s…
Detecting 1a.mzML … 2972 peaks found!
Detecting 2a.mzML … 2569 peaks found!
Detecting 3a.mzML … 1615 peaks found!
Calculating peak correlations in 470 Groups…
Calculating graph cross linking in 470 Groups…
New number of ps-groups: 3198
mSet has now 3198 groups, instead of 470 !
Generating peak matrix for peak annotation!
Polarity is set in annotaParam: negative
Ruleset could not read from object! Recalculating…
Calculating possible adducts in 3198 Groups…
Step 6/6: Successfully performed peak annotation! (2023-06-13 23:54:30.215441)
Going to the final step…

maPeaks ← FormatPeakList(annotPeaks, annParams, filtIso =F, filtAdducts = FALSE, missPercent = 1)
mSet<-Read.TextData(mSet, “metaboanalyst_input.csv”)
Error in *tmp*$dataSet : $ operator not defined for this S4 class

Read the text data into the mSet object

anal.type ← “regression”

Read text data into an mSet object

mSet ← Read.TextData(file = “metaboanalyst_input.csv”)
Error in *tmp*$dataSet : $ operator is invalid for atomic vectors

Access the data within the mSet object

data ← exprs(mSet) # or assay(mSet)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘exprs’ for signature ‘“mSet”’

Read text data using read.csv()

data ← read.csv(“metaboanalyst_input.csv”)

Create an mSet object

mSet ← list(dataSet = data)

Further processing with the mSet object…

mSet1 ← SanityCheckData(mSet)
print(mSet1)
[1] 0
mSet<-FilterVariable(mSetObj = mSet, “iqr”, “F”, 25)
Error in qs::qread(“data_proc.qs”) : Failed to open file for reading.

Does the file exist?
Do you have file permissions?
Is the file name long? (usually 255 chars)

What does it mean? There were some warnings which I was ignoring, but I think those warnings were the reason why I was not able to use FilterVariable correctly.

Appreciate the help.
Thank you!