I could group the peaks, correct the retention time, fill the missing peaks and eventually get final result visualization.
However, when I tried to use the centWave method for those high-resolution data, I could do group, but not go through the retcor step. Please refer to the following codes and error/warning message.
Retention Time Correction Groups: 1 Error in .local(object, ...) : Not enough ``well behaved'' peak groups even for linear smoothing of retention times In addition: Warning message: In .local(object, ...) : Too few peak groups, reverting to linear method
I did play with the arguments such as snthresh, peakwidth, prefilter, fitgauss, unfortunately I failed whatever I tried. The error message is:
Quote
Error in .local(object, ...) : No peak groups found for retention time correction
In addition, I tried to use obiwarp method for retention time correction after failing to use the default loess method (as shown above). Unfortunately, my desktop was down always whenever I ran the following code.
I got 10 EIC images and a tsv report file. When I looked at and compared the images with the detailed list in the tsv file, I got several problems that need to be clarified by XCMS experts here.
According to one of the EIC images, it is an extracted ion chromatogram: 433.12-433.33 m/z. However, in the tsv file, the corresponding ion's mzmed, mzmin and mzmax are 433.245461, 433.243672 and 433.272257. I wanna know why the m/z range in the EIC is much broader than the one determined by mzmax and mzmin. Is the ideal m/z range 0.3 (double of the value of argument metlin)?
A similar concern is that the retention time range (highlighted zone) used for integration appears to not match with the range determined by the corresponding ion's rtmax and rtmin.
Is there any way to find out the curve details on the EIC images (just like the legend in the retention time deviation plot, which is generated by running retention time correction)? In other words, is there any way to see which sample is contributing to a specific curve of interest on the EIC image?
On some EIC images, the highlighted area covers several obvious peaks. What is the reason for this? To my understanding, the highlighted area should only have one peak. If so, how to improve the peak picking process?
In addition, what is the default value for argument eicwidth in method diffreport?
xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden")
The message is :
Quote
Warning message: In .local(object, ...) : Fitted retention time deviation curves exceed points by more than 2x. This is dangerous and the algorithm is probably overcorrecting your data. Consider increasing the span parameter or switching to the linear smoothing method.
Do I need to re-run the correction? If so, how to increase the span parameter or switch to the linear smoothing method? Thanks for your concern in advance.
Unfortunately, XCMS comes back with the following message:
Quote
Error in file(file, ifelse(append, "a", "w")) : cannot open the connection In addition: Warning message: In file(file, ifelse(append, "a", "w")) : cannot open file 'HopkTrial_1.tsv': Permission denied
Is there any one who can help me define the reasons for the error message? Your prompt response will be highly appreciated.
According to literatures, there are so many kinds of plot to present LC/MS-derived metabolomic data such as principal component analysis (PCA), scatter plot, heatmap, volcano plot. As a green hand of xcms, I don't know how to use it for generating these plots. In addition, xcms online can present data in Cloud Plot. I wanna know whether it is possible to produce Cloud plot using xcms. If so, how to generate using xcms? I am desperately waiting for the answers for the questions. Your prompt responses are greatly appreciated in advance.
I processed the Agilent .d folder files to get the peak lists that were then saved into files in the mzData format using Mascot Distiller. Unfortunately, xcms process stopped after I ran "xset <- xcmsSet(myfiles)". The error message is "Error in if (yfilt[maxy] > 0 && yfilt[maxy] > snthresh * noise && ysums[maxy] > : missing value where TRUE/FALSE needed". Is there anyone who had similar situation and got this kind of error before? Thanks.
My samples were analyzed using HPLC (CHIP)- Agilent 6520 with MassHunter software. The size of each original data (folder with .d extension) is around 2G, which is the storage limit. So, I converted the data into mzData format using Mascot Distiller. After conversion, the file size was down to ~3M. Unfortunately, after submitting the mzData files to the XCMS online server for processing, I received a error message saying "No LC/MS data". I wanna know what I can do now. Your early responses will be highly appreciated.
One more question: if the size of my dataset (either one) is larger than 2G, do I have to install XCMS in the local computer for data analysis? Is there any alternative way to keep using the convenient XCMS online?
