Hi Elisa,

I assume you have read the vignette of IPO (https://www.bioconductor.org/packages/devel/bioc/vignettes/IPO/inst/doc/IPO.html) and reproduced the examples output. I am not sure which benefits you expect from a script on other data than the example provided by IPO.

More precisely: (i) do you have trouble running the example data or your own data because you run into some errors which you can not fix yourself? or (ii) do you get unexpected results out of IPO and want to better understand what is the idea/method behind?

Bests, Jan

Hi,

try this one out, this is a good start for your self learning jounrey :)

Script: library (xcms)

library (CAMERA)

xset

Hello Jan, yes I've read the vignette of IPO and I was able to optimize my parameters. I've actually not used examples data, I tried using my data in the first try and I was able to generated the script with IPO, using this last function:

"writeRScript(resultPeakpicking$best_settings$parameters, resultRetcorGroup$best_settings)"

However, when I try to process my data with xcms, with the parameters from IPO, I get an error. It says:

"Error in .local(object, ...) : No group information found"

I'm stuck with this error and I can't really solve it on my own, even after looking at other questions, solutions or discussions.

Thank you very much Joseph!

Why do you use the function group () two times and the retcor() two times?

xset

Sorry I made a mistake while copy/pasting

This should be fine now.

Elisa Ribeiro Miranda Antunes, so you got pretty far already. Congratulations! :) The error points at the fact that some xcms function which works on groups of samples (could be retcor()) is missing information regarding the groups or has wrong information. Did you maybe optimize the parameters with IPO on a subset of the samples and than tried to apply it to a larger set? Than the grouping information in the 'best_settings$parameters' may not fit your data anymore.

Alternatively, you have not provided any group information in the IPO step but try to apply a function which needs that. Hard to fix without knowing your experimental setup. Bests, Jan

Thank you Jan! Actually as it is only a few samples, I applied IPO in all of them. This is the script I have and that I'm trying to use so far:

The first tree functions were written using the function writeScript() from IPO.

xset

You should be able to run the 3 functions where IPO generated the pars independently. 'fillPeaks' needs grouping information (because it tries to fill missing peaks based on replicates of the same type). My guess is that you do not have any grouping information in the xcmsSet you generate. Please try to provide 'sclass' as an additional parameter to your xcmsSet call. It should be a factor indicating the groups of your samples. If you process 10 files with 5 replicates of group A and B respectively than 'gl(2,5)' would give you a reasonable input for 'sclass'. You can avoid specifying sclass explicitly when you put your input files into different subfolders (which is what the xcms people prefer I believe). Than xcms should 'guess' the grouping based on the subfolder structure. Bests, Jan

Thank you Jan! I will try that

Hi, This is a very interesting and relevant question for the entire research community working in metabolomics. Please feel free to register (for free to create a login with your Email ID!) and join the International Metabolomics Society’s Forum: http://www.metabolomics-forum.com/index.php?action=forum;?action=forum#c12 to ask more specific questions any software, database, approach and platform (mass spectrometry, NMR) issues where you can get very specific responses from expert users and researchers! Thanks again, Biswa