I have never used R for XCMS. I have always used the online version, a lot more user friendly for someone like me (not a bioinformaticist ). While I can try to extract my peak manually using R, I wanted to see if there is something I can change in the online version of XCMS that can help me extract my peak.
I have inspected raw chormatograms visually and it is definitely there, although not very highly abundant. It is present in about 60% of the samples.
Can you help me change the parameters online before I move into trying it in R?
I am trying to look at a particular mass that I know is in raw chromatograms but for some reason cannot extract it with the parameters I am putting in. I am able to extract it using Marker Lynx software, however.
I was asking that question because I have a concern regarding the data extraction. I extracted some data, job ID 4274 and there is a pretty prominent peak with a mass of 177.103, which we know is cotinine. When I look at the raw chromatograms, it is there. However, after extracting the data, it does not make the list. Maybe my parameters are not set up correctly. Is there anything you can do to help me resolve this issue?
I am unsure of how XCMS extracts ions and I would really like to understand it. For example, when the instrument takes snap-shots while running samples, one ion can come at several different masses which are a little different (under the same peak) i.e. 107.1043, 107.1057, 107.1068, etc. When XCMS extracts these ions, does it consider them separate or one and the same ion?
I need to have median peak area for something and was wondering if the results file we can download upon running data has that information? If not, is there a way for me to obtain that information?
Also, I asked a question in another post but nobody responded yet. What stastistical test is applied to look at differences between a dataset 1 and a dataset 2?
The last couple of days I have been having problems with data uploads. For some reason, each time I upload there is a different file that has a status of "Invalid MD5". Is there a way to fix this so that all the files get uploaded correctly?
I ran some ESI- data for the first time. I chose negative polarity in the settings, and didn't select any adducts under identification since there were none to choose from. However, the results table still shows positive isotopes i.e. [3][M+1]+ Is there a mistake?
p.s. job ID is: 3543
I also realized it is very possible I am reading the adducts incorrectly. Can you please explain to me what this means, what it refers to: [3][M+1]+
). While I can try to extract my peak manually using R, I wanted to see if there is something I can change in the online version of XCMS that can help me extract my peak.