out of retention time range for this sample

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out of retention time range for this sample

June 18, 2012, 12:20:31 AM

HI All,

Can someone help me with this error. I think I need to tweak the retention time in the Script...am i right if so how can i do that.

I am targeting peeks between 1m and 75 m for my work and i have getting this issue ...any suggestion please.

1: In .local(object, ...) :
getPeaks: Peak m/z:453.743311482323-453.847218882211, RT:4486.392-4502.802is out of retention time range for this sample (C:/MZdataXCMS/SA/2010_12_12 H069.mzdata.xml), using zero intensity value.

2: In .local(object, ...) :
getPeaks: Peak m/z:453.743311482323-453.847218882211, RT:4486.392-4502.802is out of retention time range for this sample (C:/MZdataXCMS/SA/2010_12_12 H072.mzdata.xml), using zero intensity value.

3: In .local(object, ...) :
getPeaks: Peak m/z:453.743311482323-453.847218882211, RT:4486.392-4502.802is out of retention time range for this sample (C:/MZdataXCMS/SA/2010_12_12 H074.mzdata.xml), using zero intensity value.

4: In .local(object, ...) :
getPeaks: Peak m/z:453.743311482323-453.847218882211, RT:4486.392-4502.802is out of retention time range for this sample (C:/MZdataXCMS/SA/2010_12_12 H079.mzdata.xml), using zero intensity value.

5: In .local(object, ...) :
getPeaks: Peak m/z:453.743311482323-453.847218882211, RT:4486.392-4502.802is out of retention time range for this sample (C:/MZdataXCMS/SA/2010_12_12 H080.mzdata.xml), using zero intensity value.

6: In .local(object, ...) :
getPeaks: Peak m/z:453.743311482323-453.847218882211, RT:4486.392-4502.802is out of retention time range for this sample (C:/MZdataXCMS/SA/2010_12_12 H081.mzdata.xml), using zero intensity value.

7: In .local(object, ...) :
getPeaks: Peak m/z:453.743311482323-453.847218882211, RT:4486.392-4502.802is out of retention time range for this sample (C:/MZdataXCMS/SA/2010_12_12 H082.mzdata.xml), using zero intensity value.

8: In .local(object, ...) :
getPeaks: Peak m/z:453.743311482323-453.847218882211, RT:4486.392-4502.802is out of retention time range for this sample (C:/MZdataXCMS/SA/2010_12_12 H083.mzdata.xml), using zero intensity value.

Thanks in advance

Re: out of retention time range for this sample

Reply #1 – June 18, 2012, 03:38:34 AM

Hi,

Quote from: "utpal_bose"

I think I need to tweak the retention time in the Script...am i right if so how can i do that.
I am targeting peeks between 1m and 75 m for my work and i have getting this issue ...any suggestion please.

1: In .local(object, ...) :
getPeaks: Peak m/z:453.743311482323-453.847218882211, RT:4486.392-4502.802is out of retention time range for this sample (C:/MZdataXCMS/SA/2010_12_12 H069.mzdata.xml), using zero intensity value.

This should be perfectly fine, the warning comes from fillPeaks().
there is a peak (as indicated by many other files) after grouping,
but in your sample this RT is 75.0467min, so beyond the "end" of the file.

Hence, there is no raw data available for fillPeaks(). Unless you expect
very important peaks at 75mins, you can safely ignore this.

Yours,
Steffen

Re: out of retention time range for this sample

Reply #2 – June 18, 2012, 05:05:28 AM

There is additional discussion of this issue here: viewtopic.php?f=8&t=258&p=727

Re: out of retention time range for this sample

Reply #3 – June 19, 2012, 11:07:51 PM

Dear Steffen,

thank you and really appreciate your reply regarding the peak issue. As i am new to R and XCMS I would like know where and how I shall change the retention time.

In this case its between 0.7 - 75 minutes (Time Range). This will be of use to me for my feature work.

############################################
Output from my Run
############################################
An "xcmsSet" object with 144 samples

Time range: 39.7-4499.8 seconds (0.7-75 minutes)
Mass range: 100.0395-982.9937 m/z
Peaks: 15263 (about 106 per sample)
Peak Groups: 0
Sample classes: SA, SP

Profile settings: method = bin
step = 0.1

####################################################

Thanks in Advance
Utpal

Re: out of retention time range for this sample

Reply #4 – June 20, 2012, 12:53:48 AM

Hi,

The peak that triggers the warning is really at the edge of the RT
that you target (It expands beyond 4500). Either ignore the warnings, or use

Code: [Select]

xcmsSet(..., scanrange=c(lower, upper) )

where lower/upper
delimit the scan numbers (!) you want to include. If you have 1Hz
acquisition rate, it'd be

Code: [Select]

scanrange=c(60, 4440)

to use 1m-74m where the problem should be not occuring anymore.

Yours,
Steffen

Re: out of retention time range for this sample

Reply #5 – June 21, 2012, 08:12:40 PM

Dear Steffan,

I am having a same problem when i run the script, I modified the code to
### finds peaks in NetCDF
xset <- xcmsSet(scanrange=c(60, 8000.99))

and i need xcms to look between 1 min and 80 mins.

It still comes out with the message...
warning - out of retention time..