As mentioned of XCMS preprocessing document, the argument of group(), sleep, is enabled to plot the corresponding peaks. My questions are:
1. Is the method "density" the default grouping ? 2. What's the definition of density (Y-axis)? Is it normalized? If YES, what is the value normalized? Why the corresponding value is usually small? 3. What's the definition of the solid line in this figure? Peaks are plotted as points showing it relative intensity. And what's meaning of the solid line?
I am beginner of studying how to manipulate and process the LC-MS data. I am curious how can I manually apply XCMS to access LC-MS data in processing of feature detection, retention time correction, peak alignment (grouping), peak filling just like workflow as XCMS Online. To learn the manipulation and processing of the LC-MS data, I apply the data from Saghatelian et al. which consists of 6 knock-out and 6 wild-type samples. I upload and process these data through XCMS Online. The corresponding log shows as below:
According to previous code, total number of peaks is 4721 generated by
xcmsSet constructor which is not consist with the result shown in previous log file. I guess that XCMS automatically construct the xcmsSet object. The procedure maybe contain several individual steps such as xcmsRaw, retcor, group. How can I reproduce the same results provided by XCMS Online?[/list] I had also tried to detect feature by using the following instructions
The number of peaks detected is also 3515 which is consist with XCMS Online log file. So I repeat the previous code for data loading and peak detecting of each sample. The following problem is how to do retention time correction? According to help of XCMS document, I found instruction of retcor.obiwarp. However, this instruction belongs to xcmsSet-class method. How can I perform the following retention time correction? This really confused me. Please give me your advising. Thanks for all.