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
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.
Hello, I'm unfamiliar with R and have had little success getting what I'm looking for from XCMS. My goal is to obtain a data matrix of aligned (untargeted) components and retention times, with the data made up of peaks areas. The data is from an Agilent LC-QTOF instrument. I have transferred the data files into mzData format and saved it in the same directory where R is installed. My first problem is - I could not able to upload data files for analysis. It always comes with a error message.
Does anyone happen to have a set of example command lines they can copy and paste to me to complete a LC/MS data analysis obtained from LCMS system?