I'm attaching the traceback and some of the data in xset below. There are files, but after i try the few
First i ran the scripts as below
> xset2 <- retcor(
+ xset,
+ method = "obiwarp",
+ profStep = 1,
+ plottype = "deviation",
+ center = NULL,
+ col = NULL,
+ ty = NULL,
+ response = 1,
+ distFun = "cor_opt",
+ gapInit = NULL,
+ factorDiag = 2,
+ factorGap = 1,
+ localAlignment = 0,
+ initPenalty = 0)
center sample:
Processing: Error in if (!file.exists(object)) stop("xcmsSource: file not found: ", :
argument is of length zero
> traceback()
11: .local(object, ...)
10: xcmsSource(filename)
9: xcmsSource(filename)
8: xcmsRaw(object@filepaths[center], profmethod = "bin", profstep = 0)
7: .local(object, ...)
6: retcor.obiwarp(object, ...)
5: retcor.obiwarp(object, ...)
4: do.call(method, alist(object, ...))
3: .local(object, ...)
2: retcor(xset, method = "obiwarp", profStep = 1, plottype = "deviation",
center = NULL, col = NULL, ty = NULL, response = 1, distFun = "cor_opt",
gapInit = NULL, factorDiag = 2, factorGap = 1, localAlignment = 0,
initPenalty = 0)
1: retcor(xset, method = "obiwarp", profStep = 1, plottype = "deviation",
center = NULL, col = NULL, ty = NULL, response = 1, distFun = "cor_opt",
gapInit = NULL, factorDiag = 2, factorGap = 1, localAlignment = 0,
initPenalty = 0)
Then i inspect the data in xset.
> str(xset, max.level = 2)
Formal class 'xcmsSet' [package "xcms"] with 15 slots
..@ peaks : num [1:6117, 1:11] 379 421 397 471 235 ...
.. ..- attr(*, "dimnames")=List of 2
..@ groups : num [1:116, 1:9] 181 236 249 255 279 ...
.. ..- attr(*, "dimnames")=List of 2
..@ groupidx :List of 116
..@ filled : int(0)
..@ phenoData :'data.frame': 46 obs. of 1 variable:
..@ rt :List of 2
..@ filepaths : chr [1:46] "G:/tissue/mzxml/np/neg/CASE/D N 1.mzXML" "G:/tissue/mzxml/np/neg/CASE/D N 2.mzXML" "G:/tissue/mzxml/np/neg/CASE/D N 3.mzXML" "G:/tissue/mzxml/np/neg/CASE/DN 4.mzXML" ...
..@ profinfo :List of 2
..@ dataCorrection : int(0)
..@ polarity : chr(0)
..@ progressInfo :List of 15
..@ progressCallback:function (progress)
..@ mslevel : num(0)
..@ scanrange : num(0)
..@ .processHistory :List of 46
> head(xset@peaks)
mz mzmin mzmax rt rtmin rtmax
[1,] 379.1944 379.1942 379.1948 97.324 79.794 112.823
[2,] 421.2051 421.2044 421.2053 108.454 87.215 119.562
[3,] 397.1605 397.1600 397.1609 112.486 92.272 124.966
[4,] 471.1973 471.1968 471.1977 112.823 92.609 121.588
[5,] 235.1809 235.1807 235.1810 120.573 105.423 128.338
[6,] 463.2157 463.2154 463.2162 121.249 108.454 129.683
into intb maxo sn sample
[1,] 63585.88 63243.50 18469 281 1
[2,] 126455.21 125712.75 20504 184 1
[3,] 112149.18 112028.20 16132 697 1
[4,] 111377.42 111166.17 19105 354 1
[5,] 128713.22 128676.36 31172 1242 1
[6,] 62646.78 62619.22 10310 509 1
>
I still couldn't find out where is the bug you mentioned.
However, If i dont run the specify center=NULL, is it safe to say its running in NULL ?
Thanks.