Hi,
I would like to process my data but not using fillpeaks. Hereafter is the return I got:
> reporttab<-diffreport(xset2,"échantillons","pools","urines_par_ech",10,metlin=0.15,h=480,w=640)
Erreur dans .local(object, ...) : NA values in xcmsSet. Use fillPeaks()
any idea how to circumvent this problem and to get to the reporttab step?
many thanks
jc
JC,
Not quite sure why you wouldn't want to use fillPeaks as you will have lots of NA's but...
library(faahKO)
gxs<-group(faahko)
foo<-peakTable(gxs, file="~/Desktop/temp")
This will give you a data frame, foo, that you can use in R and a tsv file which will be called temp.tsv
hope it helps,
Paul
Hi JC,
the diffreport function calculates the fold changes between two samples for every feature.
If in one sample the value is NA (meaning the feature could not be detected or the feature intensity was lower than your filtering settings),
then the fold change can't be calculated.
For those cases the fillPeaks function was written and works quite well.
Carsten
thank you for you both to answer,
my reason why I don't want to get fillpeaks is that I performed a large scale LCMS analysis, running over 800 samples within 9 different batches; then I need to apply a batch correction algorithm (van der Kloet et al) which does not like peaks filled; In fact, I will have to discard peaks that missed in 60% of the pool samples prior applying the correction; as an additional difficulty, I also need CAMERA to run, and it does not like 'NA'. How can I thus run CAMERA with NAs in data frame?
hope my explanation is clear...
thanks!
jc
Hi Jc,
so do you need the diffreport function or are you fine with the peaktable generated by the script from Paul?
And for using CAMERA at which step if complains about the NA values?
The only function I could imagine would be annoteDiffreport, which uses the diffreport and therefore were are back at the start of this thread ;)
But all other functions should work with NA values.
If you don't want to use the wrapper functions,
you find in every manpage some code examples for the "normal" script based analyis.
If you need help within any function, just write me a note.
Perhaps in the CAMERA sub forum that so that we not "pollute" this one :)
Carsten
JC,
As Carsten said CAMERA should be ok with everything not filled. Just gave a quick test of a none filled xcmsSet object with CAMERA on default parameters. Everything worked ok. There was a warning on the correlation about NA's but the length will probably get chopped. Again as Carsten said probably better to start a new thread in the CAMERA section, bad on me. Also if you want to additionally remove samples that are not seen in 60% of the samples then I would recommend to set minFrac in the group-ing to 0.60 as this will do this automatically for you in the function.
Hope it helps,
Paul