Skip to main content ↑ ↓

Show Posts

This section allows you to view all Show Posts made by this member. Note that you can only see Show Posts made in areas you currently have access to.

Messages - lixiyan

1
XCMS / Re: Wrap XCMS dataset in a package?
Ralf,
Thanks for the quick reply. I did save the xcmsSet the way you said but didn't realize it could be used that way.

best,
Xiyan
2
XCMS / Wrap XCMS dataset in a package?
Hi,
I was wondering if there is an R utility to wrap XCMS datasets in a package? Something like the FaaKO datasets in XCMS installation. This package would be portable and convenient for my collaborators to do followup stat analysis.

thanks,
Xiyan
3
XCMS / Re: Read peaks list in text format directly to XCMS
Ralf,
Thanks for the reply, that's quick!

I am using Thermo Exactive. The thing is that I am using a home-made program to do centroiding which only produces peaks list in text file.

I'll try Fileconverter and post my experience out of it.

Xiyan
4
XCMS / Read peaks list in text format directly to XCMS
Hi,
I wonder if there is a way to read my centroid peaks list files directly for XCMS analysis. My peaks list format (.txt) is described at the end. I think it contains all info that XCMS needs for analysis purpose.

Another way is to compile these lists into mzXML format. Is there a convenient parser already there? My google search didn't turn out good solution to this.

Any suggestion in either way is greatly appreciated.

Xiyan


###The format of my peaks list in .txt#############
............
Scan#: 8
Ret.Time: 0.103439
IonInjectionTime(ms): 250
TotalIonCurrent: 288848
BasePeakMass: 104.1073965
BasePeakIntensity: 108806
83.06096   652.943
84.04497   1627.873
84.05624   275.127
.............
Scan#: 9
Ret.Time: 0.117677
IonInjectionTime(ms): 250
TotalIonCurrent: 90145.1
BasePeakMass: 255.2325484
BasePeakIntensity: 52749.7
83.02424   98.579
101.24509   105.154
103.97359   103.052
107.27591   106.289
107.41876   98.873
111.60914   120.939
119.03371   1083.924
............