Skip to main content ↑ ↓

Topics

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

Topics - panos

1
XCMS / Any possible info about a retcor error?
Dear xcms developers,

I would like to ask (I know it is a quite general question though...) what might be causing the following errors (not at the same time but using different parameters) in a 2nd pass of retcor after a first data grouping:

Code: [Select]
Error in stepfun(rtcor[[i]][-1] - diff(rtcor[[i]])/2, rtcor[[i]] - rtdevsmo[[i]]) : 
  stepfun: 'x' must be ordered increasingly
Code: [Select]
Error in quantile.default(abs(rtdevsmo[[i]]), 0.9) : 
  missing values and NaN's not allowed if 'na.rm' is FALSE
I am trying to process 75 samples of CE/MS data in netcdf format, after filtering out 2 time intervals from the beginning and the end of the scan range. I know that xcms was not initially developed for CE/MS data but it has been sucesfully used in a couple of publications. I should mention that these errors occur in any (steps, snthresh) configuration (matchedFilter), other than the default (steps=1, snthresh=10). For example I have tried (steps=1, snthresh=7), (steps=3, snthresh=10), (steps=3, snthresh=7), (steps=2, snthresh=7) and (steps=2, snthresh=10) is currently running. I am using sigma=7 (found to be good for my data after some visual inspection). The errors are always occuring in an iterative grouping/rt correction procedure, on the 2nd iteration (initial grouping bw=30 or 50, next values 30 or 20). The parameter steps=3 was suggested in a publication using xcms with CE/MS data.
These errors was not occuring in the previous xcms version I had on my system (1.23.1), when using several parameter sets like the above. Thanks in advacne for any replies!

Panos
2
XCMS / Difference of minfrac and minsamp in group function
Dear xcms developers,

I would be grateful if you could explain the difference between the minfrac and minsamp parameters in the group function of xcms. A small example would also be appreciated. I believe I correctly understand the minfrac parameter (the "percentage" of samples that need to have proper peaks under a group so as to define a meta-peak?), but can you please also explain the minsamp parameter? In addition, if the minsamp parameter is increased, naturally the number of peak groups decreases. How advisable/useful is to increase minsamp in a dataset of 75 samples but including 16 different classes? (CE/MS). Thank you in advance for your help.

Panos
3
METLIN / Install METLIN locally
Hello,

I was wondering if there is a version of METLIN (even a limited one) that can be downloaded and installed on a local server (using SQL dumps or other flat files), similar to the ChEBI database. As I am trying to build an analysis/annotation pipeline for the lab I work, it would be really useful. Otherwise, is there a programmatic access to METLIN outside the web interface? Thanks in advance!

Panos
4
CAMERA / runParallel slot in xsAnnotate
Hi CAMERA developers,

I would like to ask about the purpose of runParallel slot in the xsAnnotate object of CAMERA. As I am processing a rather large dataset, I would like to know if I can take advantage of the mutliple cores of the machine I am working. Thank you in advance!

Panos