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Messages - Ricca

31
XCMS / METLIN information extraction
Hi, is there a way to manually generate the link to Metlin database without using diffreport method?? I see in the manual that is possible when you have an MS^n experiment while I have only a MS experiment with no fragmentation.

Best
32
XCMS / Re: fillPeaks and sn-values
So it right to assume that prefilter works fisrt  and than the S/N filter.

Using the example of gunnar:
Quote
I lowered snthresh to 50 and prefilter to c(3,3333) and that helped.

First the prefilre select features accordining to c(3, 3333), three peaks with an intensity of 3333 counts each, than the S/N filter exclude all the peaks below a s/n of 50.
Is that right??
33
XCMS / Re: fillPeaks and sn-values
I have not clear in my mind how prefilter and snthresh works together. So, which filter is master and which is slave?? I can I control their interaction?
34
XCMS / Re: Pbroblem with large data set and loop
Paul,
maybe I discovered the problem. I tried to execute the R code in another linux machine and I haven't still had any problem... I hope the problem is only in the computer.

I'm sorry I made you waste your time and I would like to thank you for your help and your suggestion.

Best regards
Riccardo

P.S. I have a further question, I have no experience about the S4 programming rule and I see that the xcms library is written using S4 object. Where can I find information about S4 object programming?? For example how can I perform an easy loop code such this with S4 object?

Code: [Select]
for(i in 1:3){
    xset[i] <- xcmsSet(data.set[i], method="centWave",
                       polarity="positive", ## prefilter=c(3,5000),
                       ppm=10, snthr=1500, peakwidth=c(4,15))
    foo <- c(xset[i])
}
35
XCMS / Re: Pbroblem with large data set and loop
Paul,
now it works fine, all the files are characterized by a 0 and so there are no corrupted file... but the problem still remain...

Do you think is possible that the problem is the PC?? I work with a quad core, 7gb ram, ubuntu 10.04 workstation.
36
XCMS / Re: Pbroblem with large data set and loop
Paul,

Quote
Just change the cdf to what you need.
I follow your instruction but apply give to me a bad response:

Error in apply(AllCDFs, 1, CheckCDFfile, type = ".mzdata") : dim(X) must have a positive length

Quote
You're loading the file that had the problem and not some other one?
Yes

Quote
I would have a look with something else like OpenMS or mzViewer just to check the file loads.
I used mzMine and all works

I relly have no idea.... :?:

Ricca
37
XCMS / Re: Pbroblem with large data set and loop
I try the first code:
Code: [Select]
rampid<-xcms:::rampOpen("17_GS34_A.mzdata")
rampid
[1] -1
Code: [Select]
rampHead<-xcms:::rampScanHeaders(rampid)
Error in xcms:::rampScanHeaders(rampid) : invalid rampid

For the second code you wrote I have a doubt about its use because it is for a .cdf file while I have an .mzdata
38
XCMS / Pbroblem with large data set and loop
Hi, I have a problem to work with a large data set (about 200 samples). In particular I have a problem to creaete the xcmsSet:

Code: [Select]
xset <- xcmsSet(data.set, method="centWave",
                    polarity="positive", ppm=10, snthr=15, 
                    peakwidth=c(4,15))

In particular, after a few times, about 2 hours, I encountered  several errors such as:

Detecting mass traces at 1o ppm ...
 % finished: 0 10 Error in .local(object, ...) :
  m/z sort assumption violated ! (scan 376, p 63, current 100.9567 (I=1708.65), last 843.6795)

or

17_GS34_A.mzdata: Error in rampSIPeaks(rampid, scans, scanHeaders$peaksCount[scans]) :
  unexpected end of peak list
Calls: xcmsSet -> xcmsRaw -> rampRawData -> rampSIPeaks -> .Call

I have no idea about the problem, do you have any suggestion??

I also tryed to use a loop to create an xcmsSet object:
Code: [Select]
for(i in 1:3){
    xset[i] <- xcmsSet(data.set[i], method="centWave",
                       polarity="positive", ## prefilter=c(3,5000),
                       ppm=10, snthr=1500, peakwidth=c(4,15))
    foo <- c(xset[i])
}

but the R console say: Error in xset <- xcmsSet(data.set, method = "centWave", polarity = "positive",  :
  object of type 'S4' is not subsettable

Best
39
XCMS / Re: Exclude masses
Thanks for you suggestion!! Now the code is right.

Best
40
XCMS / Re: Exclude masses
I tryed the example of the link you suggested:
Code: [Select]
(xset1 <- xset[which(xset@peaks[,"mz"]<600 & xset@peaks[,"mz"]>100),] )
but the R consol give this error:
Code: [Select]
Errore in xset[which(xset@peaks[, "mz"] < 600 & xset@peaks[, "mz"] > 100),  : object of type 'S4' is not subsettable

Do you have any further suggestion?? :?:
42
XCMS / Intermediate steps
Hi, is there a way to save the intermediate steps of the xcms pipeline?? Could be very helpful since some operations (xcmsSet, retcor.. ) are very long and time-consuming.

Best
Riccardo
44
XCMS / Exclude masses
Hi to everybody, I'm starting to work with xcms with a lot of satisfaction but I still have some doubt. In particular I haven't still discovered a parameter that allow me to exclude some masses from my analysis. Do you have any suggestion??

Best
Riccardo