Warning message from running retention time correction

September 18, 2013, 02:09:09 PM

I got warning message after running the following code:

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.

Best wishes,

Jeff

Re: Warning message from running retention time correction

Reply #1 – September 19, 2013, 01:02:44 PM

Jeff,

Have a look at

Code: [Select]

help("retcor.loess")

This is the help/man page for the retcor function. We have different methods within the function you can choose, such as the linear method.

The span parameter is very sensitive so play carefully with it. Think of it as smoothing for the alignment.

Code: [Select]

xset2 <- retcor(xset,  family = "symmetric", plottype = "mdevden", span=0.2, smooth ="loess", missing=1, extra=1)
## or if you want linear
xset2 <- retcor(xset,  family = "symmetric", plottype = "mdevden", span=0.2, smooth ="linear") ## not recommended

Also try and have a play with missing and extra. They may help you get a good alignment.

Finally, have a look at the obiwarp alignment. I'll let you read the manpage and paper but basically to get it running it'll look something like this

Code: [Select]

xset2<-retcor(xset, method="obiwarp", plottype ="deviation")

Hope it helps,

Paul