vignettes/quantificationParameters.md

In ELELAB/lipidQ: Lipidomics Analysis Tool

title: "Parameters" author: "André Vidas Olsen" date: "2018-04-15" output: html_document vignette: > %\VignetteIndexEntry{Vignette Title} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

Introduction

This vigentte will focus on describing the different parameters in regards to the quantification procedure in LidpiqQuan.

Number of replicates

LipidQ contains a section for specifying the number of replicates in the input intensity data. If the input text is set to 1, this means that there is only the original sample extract, whereas setting the number to 2 means 2 replicates, 3 means 3 replicates etc. Also, in this field, the user can specify whether the input intensity data contains replicates in the blank extracts or not. This is done by using the checkbox marked as 'Blank contains replicates'.

Number of instances threshold & Threshold of instance

Below the field of specifying the number of replicates, the user can also specify two parameters for filtering out unrealiable measurements. This is done by using the 'Threshold of instance' and 'Number of instances threshold' fields in LipidQ. In the 'Threshold of instance' the user can specify what level of intensity will be considered as 'real signal'. In the 'Number of instances threshold' the user can specify how many of the replicates in a given sample that should have a value above the 'Threshold of instance' before the sample in question will be considered to have a 'real' signal.

Multiply MS1 columns by a factor (for LipidX users)

In cases where a low mass range and high mass range has overlapping parts, a multiplication factor will be needed for LipidX users. The reason is that LipidX takes the average of the overlapping and non-overlapping part of the low and high mass range, resulting in a division factor of 2 for some lipids, since they will not be in the overlapping part of those two overlaps. If this is the case, then the "Multiply MS1 columns by a factor (for LipidX users)" checkbox should be marked. A file containing every classes which intensity values needs to be multiplied should be included by using the "Browse..." button below "Choose the list of classes to be multiplied (.csv-file)" and selecting the file. Finally a multiplication factor should be selected in the "Set multiplication factor" field, which specify the number to multiply each classes with.

Spike ISTD

Filter types

LOQ

Limit of quantification (LOQ) is a threshold setting which specifies whether the quantification of a given lipid/species is high enough to be considered as measurable (see parameters vignette).

Threshold for rounding down to zero for mol% species:

ELELAB/lipidQ documentation built on Feb. 24, 2020, 12:54 a.m.