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oh, parameters

:? 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?

Re: oh, parameters

Reply #1
Hello,

I am new as well, but offer some help.

[quote author="luoluopig"]:? , bw argument in retention time correction, what bw stands for. [/quote]

Did you read this part in the documentation of xcmsPreProcess.pdf? It is in the doc folder of where the xcms
library was installed in your version of R.

"After retention time correction, the initial peak grouping becomes invalid and is
discarded. Therefore, the resulting object needs to be regrouped. Here, we decrease the
inclusiveness of the grouping using the bw argument
(default 30 seconds)."

[quote author="luoluopig"]>reporttab[1:4, ], what this 1:4 is?[/quote]

More from the same document.

"A report showing the most statistically significant differences in analyte intensities can be
generated with the diffreport method. It will automatically generate extracted ion chro-
matograms for a given number of them."

The [1:4, ] is R syntax for operating (in this case printing) on the rows 1 through 4 of a matrix and the blank after the comma is for operating on all the columns of the matrix.

[quote author="luoluopig"]Second, if no error message, does that mean the results obtained from XCMS is relaible;[/quote]

As for reliability, do no use the matchedFilter algorithm when you can use the centWave feature finder. It is specified under the parameter ...

>xcmsSet( ..., method = 'centWave', ...) and you should try to optimize the parameters.

Best of luck,
--Chris

Re: oh, parameters

Reply #2
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?

Re: oh, parameters

Reply #3
Some of your questions are R based questions, these I can recommend a good R book. Like S poetry http://http://www.burns-stat.com/pages/spoetry.html (commercial version of R is S). It's quite big but it's good and very helpful.
For the pure xcms stuff, there is now quite a lot of material online distributed through out the old mailing list and other sites. In R you can always ask for help on a function by typing
Code: [Select]
?xcmsSet
?group
?retcor
#etc
These pages will tell you how the function works and what parameters are needed. Of course there is also the xcms and centWave paper which are good to read after you have played with the software a bit. Finally, a lot of the developers give talks on xcms thought out the year so keep your eyes open for these.

hope these help

Paul
~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page

Re: oh, parameters

Reply #4
I am really grateful. Tears in my eyes.