I am interested in generating the images from Ralf's Bioinformatics paper in 2008 (Highly sensitive feature detection for high resolution LC/MS). Specifically pages 5,9 and 10 of the m/z domain and the corresponding chromatogram with applied wavelet. If anyone has done this before, I would greatly appreciate a point in the right direction.
Can I extract this data from R as the algorithms are being applied, or will I need a separate software for this generation?
1. Does the XCMS generated Excel data include all peaks identified, or just the ones it considers "different" enough based on the statistical tests performed? I've been thinking that XCMS removes the statistically similar peaks, but with the more reading I do I believe I am wrong. So, XCMS highlight what is different between samples based on the t-test and p-value, but it also gives you information on what is the same? Or no?
2. And, when dictating the bandwidth parameter in the second group command (xset2<-group(xset2, bw=10)) what does this actually dictate and when is it necessary to change it?
I was wondering what the acceptable +/- ppm window is when identifying a compound? I am obtaining accurate mass data with an LC-ESI-TOF-MS and I know XCMS searches metlin within 0.15. Just wanted to get the general opinion before I start searching other databases- Thank you!
I have a question about the .tsv file "n peaks" column and its correlation with the corresponding EIC.
Sometimes, it appears that they do not correlate, for example- the "n peaks" column will indicate "0" peaks for a group when I can see a peak in the EIC (at 10^4 abundance, which for some peaks indicates "1" and not "0"). Is this caused by a default s/n value or threshold that I have somewhere in my workup?
Does anyone know what program was used to generate Figure 5 (A) in this paper? I am looking to export my data to make a similar image and cannot find it- thank you for any help! http://www.nature.com/nmeth/journal/v4/ ... h1038.html
I was wondering if there is a way to search the KEGG database similar to the search scripts for METLIN through XCMS? And if not, (I am also new to the KEGG database) how can you search KEGG by molecular weight? I have been searching and no luck- thank you for any help!
