Hi, Paul, My data is HPLC. My sample size is quite small (3 replicates for one sample). I guess I could take off the retention time correction for my data and see what gonna happen. I just realized XCMS on R program uses "rector" as a method for retention time correction. But in XCMS online the default is "orbiwarp". The other two options left are "peakgroup" and "none'. I assume none of these three methods are same with "rector'? Not until you mention, I collected QC data. But I had no idea how you could use QC samples to do what you said on XCMS online. Where is this CV filter on XCMS online?
Hi, Paul, Thanks for your reply! That was very thoughtful. The retention correction I used was obiwarp with a step size 0.1. Do you think I should try a larger step size? I did see a lot of isotopic peaks show up as significant peak instead of mono. But I really doubt they would be another compound. A mass spectrometrist? a very delicious title. I will try my hardest to be one. Thanks, all follows. Without your help, nothing could be done by me.
I think I was wrong. They did show up in the whole peak list. But I was looking at the filtered list. So I saw the isotopic peak showing up as significant peak but not the [m] peak. If it is the situation you said, the question become, at the situation of only isotopic peak showing up as a significant feature, the related feature [m] is not considered as significant feature, right?
Hi, Jan, Thanks for your answer! That's really helpful. But I guess I did not describe my questions clearly. in your reply: >So you should have >[317][M]- >[317][M+1]- >[317][M+2]- >that belong together... That is exactly what I was wondering, how could only [317][M+2]- showed up as a significant peak in the list? where are [317][M]- and [317][M+1]- peaks?
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.
Hi, Paul, The way I put my folders was exactly same with the way you showed me. So I tried demo data (faahKO) I downloaded from bioconductor: after I typed > getwd() it came out fine. However, when I typed >sampclass(faahKO) I got an error saying" Error in sampclass(faahKO) : error in evaluating the argument 'object' in selecting a method for function 'sampclass': Error: object 'faahKO' not found"
I don't understand. The getwd already showed the correct path of faahKO folder. How could I still get this error? Do you have any idea what might be wrong there?
Hi, Paul, After I typed xcmsSet().The error says " directory tree must be level". How you guys put your folders in a diretory tree? Could you please tell me the software you are using to build a directory tree? Thanks!
Hi, Paul, When you said "testsplit"has been made", what does that mean? Every time before I run xset, I just change work directory. Is there anything else I need do? Thanks!
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",""
Thank you very much! I read couple of times that pdf file. But somehow i still can't fully understand it. How you guys got it so fast? I figured there are some backgrounds underneath missing from my knowledge. Can anybody light me up?
:? 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?
