Solvent:Article Title: Metabolic Dysregulation of the Lysophospholipid/Autotaxin Axis in the Chromosome 9p21 Gene SNP rs10757274
Article Snippet: .. XCMS parameters and R-script # all samples setwd("C:/myData") myClass1 <- "c" myClass2 <-"sol" # peak picking using wavelet algorithm for peak detection (centWave) xset <- xcmsSet (method="centWave",ppm=10, peakwidth=c(10,120), snthresh=5, prefilter=c(10,20000), integrate=1, mzdiff=0.001, fitgauss=FALSE, noise=20000, scanrange=c(1,11485)) # peak alignment xset <- group(xset, bw=30, mzwid=0.005, minfrac=0.5, minsamp=1) # retention time correction xset <- retcor(xset, method="obiwarp", profStep=0.05, response=20, center=1 ,plottype="deviation") #re-align xset <- group(xset, bw=3, mzwid=0.005, minfrac=0.5, minsamp=1) # fill in missing peak data xset <- fillPeaks(xset) # output results reporttab <- diffreport(xset, filebase="output") LipidFinder Parameters Parameter Parameter descritption Expected Data Type Current value firstRepOffset This is the index of the first sample, first replicate column Integer(>3) 3 numberOfSamples The number of samples in the experiment integer (>0) 49 numberOfTechReps The number of replicates of each sample integer (>0) 1 numberOfQCReps The number of QC replicates in the input file(s) integer (>=0) 0 numberOfSolventReps The number of solvent replicates in the input file(s) integer (>=0) 5 filePolarityMode File Polarity Mode (P: Positive mode files columnType The type of column used for LC (PO: Polar QCLowRSD Lower relative standard deviation cut off integer (>0 AND QCLowRSD AND <100 50 removeSolvent Solvent removal toggle (TRUE: Remove solvent intensity solventFoldCutOff The minimum fold difference greater than the solvent intensity a sample replicate intensity must be in order to be considered significant enough to process further Float (>0.0) 3 intensitySignificanceCutOff The level at which the intensity of a sample reading is significant enough to process Integer (>0) 1 mzFixedError The fixed error allowable when observing a mass Float (>0.0) 0.0005 mzSizeErrorPPM The mass size dependant PPM error to add to the fixed error integer (>0) 4 peakMaxRTWidth The maximum allowable retention time (mins) a single lipid peak can span Float (>=3*peakAdjacentFrameMaxRT ) 0.003 Parameter Parameter descritption Expected Data Type Current value peakMinFoldCutOff The minimum fold difference greater than the adjacent candidate frame's intensity that the current frame intensity must be in order for the current frame to be considered part of a peak. ..
Standard Deviation:Article Title: Metabolic Dysregulation of the Lysophospholipid/Autotaxin Axis in the Chromosome 9p21 Gene SNP rs10757274
Article Snippet: .. XCMS parameters and R-script # all samples setwd("C:/myData") myClass1 <- "c" myClass2 <-"sol" # peak picking using wavelet algorithm for peak detection (centWave) xset <- xcmsSet (method="centWave",ppm=10, peakwidth=c(10,120), snthresh=5, prefilter=c(10,20000), integrate=1, mzdiff=0.001, fitgauss=FALSE, noise=20000, scanrange=c(1,11485)) # peak alignment xset <- group(xset, bw=30, mzwid=0.005, minfrac=0.5, minsamp=1) # retention time correction xset <- retcor(xset, method="obiwarp", profStep=0.05, response=20, center=1 ,plottype="deviation") #re-align xset <- group(xset, bw=3, mzwid=0.005, minfrac=0.5, minsamp=1) # fill in missing peak data xset <- fillPeaks(xset) # output results reporttab <- diffreport(xset, filebase="output") LipidFinder Parameters Parameter Parameter descritption Expected Data Type Current value firstRepOffset This is the index of the first sample, first replicate column Integer(>3) 3 numberOfSamples The number of samples in the experiment integer (>0) 49 numberOfTechReps The number of replicates of each sample integer (>0) 1 numberOfQCReps The number of QC replicates in the input file(s) integer (>=0) 0 numberOfSolventReps The number of solvent replicates in the input file(s) integer (>=0) 5 filePolarityMode File Polarity Mode (P: Positive mode files columnType The type of column used for LC (PO: Polar QCLowRSD Lower relative standard deviation cut off integer (>0 AND QCLowRSD AND <100 50 removeSolvent Solvent removal toggle (TRUE: Remove solvent intensity solventFoldCutOff The minimum fold difference greater than the solvent intensity a sample replicate intensity must be in order to be considered significant enough to process further Float (>0.0) 3 intensitySignificanceCutOff The level at which the intensity of a sample reading is significant enough to process Integer (>0) 1 mzFixedError The fixed error allowable when observing a mass Float (>0.0) 0.0005 mzSizeErrorPPM The mass size dependant PPM error to add to the fixed error integer (>0) 4 peakMaxRTWidth The maximum allowable retention time (mins) a single lipid peak can span Float (>=3*peakAdjacentFrameMaxRT ) 0.003 Parameter Parameter descritption Expected Data Type Current value peakMinFoldCutOff The minimum fold difference greater than the adjacent candidate frame's intensity that the current frame intensity must be in order for the current frame to be considered part of a peak. ..
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