Hi, I know someone asked this question before. But I am still confused for understanding isotope information. i.e. one of my features has a "feature number" 3 and under "isotope"column, it shows me "[317][M+2]-" (negative polarity) for this number 3 feature. So first, when there is something showing up in isotope column, like feature 3 here, it means feature 3 has isotope peak of [M+2] (2 means?) and this "[317]" means that the feature with a feature number 317 is the isotope peak of feature 3? But it did not make sense, when I checked the feature 317 in the table. so what on earth this 317 means? Will isotopic peaks be listed in the table or not? And what kind of parameters was used to filter isotopes, don't a lot of compounds having isotopes? why this important? Can anyone help me answer this question? Thanks!
This is my first time use of XCMS online. But "select stored dataset and "view/edit" parameter did not work. I mean, when I clicked these buttons, nothing happened,no windows pop out , instead the computer was freezing, and I even could not submit the job once this freezing happened. Do you guys no why? Thanks! My computer is windows 7 and 8Mb memory.
Dear all, I tried to split my data with recipe on cookbook, however, had no success. My data is in the file called: testsplit. there are four samples in this file:HG2onedsili100, HG2twosili100,HG2threedsili100,HG2pwm and HG2pww. Each sample has triplet runs. Here are script I used and error I got:
>sampclass(testsplit) <- c("HG2onedsili100","HG2pwm","HG2pww", "HG2threedsili100","HG2twodsili100") Error in sampclass(testsplit) <- c("HpG2onedsili100", "HpG2pwm", "HpG2pww", : object 'testsplit' not found
then I did following: >sampclass<- c("HG2onedsili100","HG2pwm","HG2pww", "HG2threedsili100","HG2twodsili100") > table(sampleclass)
no errors, however error showed up in xsplit: >xslist <- split("HG2onedsili100","HG2pwm","HG2pww", "HG2threedsili100","HG2twodsili100", f=sampclass(HG2onedsili100","HG2pwm","HG2pww", "HG2threedsili100","HG2twodsili100")) Error: unexpected string constant in "xslist <- split("HG2onedsili100","HG2pwm","HG2pww", "HG2threedsili100","HG2twodsili100", f=sampclass(HG2onedsili100",""
:? It never stopped bother me, the parameters. First, I don't know the exact meaning of some parameters. For example, bw argument in retention time correction, what bw stands for. >reporttab[1:4, ], what this 1:4 is? Second, if no error message, does that mean the results obtained from XCMS is relaible; how could I know I did not overshoot data. Can anyone please recommended me a book talking about how to set up parameters for data analysis with XCMS?
