2 ;;; GC/MS : gas chromatograph / mass-soec
4 ;;; time / ion (2d graph)
6 (talk :name
"philip dixon"
9 ;; spectral fingerprints
12 ;; concentrations w/ ID'd compounds
14 (def data
(2d :x time
:y signal
) )
18 PCA of euclidean distance matrix
19 (70+ diff distance measures
)
21 (traditional-chocie: euclidane distance
)
22 (decision (or tradition arbitrary
)) )
25 (usually location-invariant
)
26 (this might not be true
! (2->3 not same as
200-
>201))
28 (weighted distance measures
,
29 (incorporation mean-variance relationship
)
31 (defun canberra-dsitance (x y
) (sum (/ (abs (- y z
))
34 (:property post-weight
, distance unchanges by metabolite-spec scaling
)
36 (choose distance-measure
39 (good-chars (consistent across choice of metabolite
)
42 weighting seems to be more impactful than selectino of distance
44 (robustness across metabolite within distance measure
)
47 (extensioon below-limit-of-detection
, usually fixed imputation
(more a LOQ than LOD case
)
48 (manage by increasing variation of measurement
, in essence down-weighting
))
50 (summary var-mean relationship helps selection of distance measure
51 plus
: incorporates lower precision of below-LOQ values
)
55 (talk :presenter
"Heike Hofmann"
56 :title
"itneractive grahics with metabolomic data preprocessing"
60 (extract peaks in GC-MS
)
61 (quant amount in the peaks
)
62 (grou in metabolite profesil
)
68 (standard sensible selection using assumption of baseline overall noise
)
70 (sumamrize AUC for peak
, sum for a metabolite
)
71 (normalize across metabolutes
)
76 GOLM
(not updated since
2004))
77 (example 4 bio reps arabidopsis WT and genotype
79 (compare (old preproc Msfacts RT matching
, normalized to ISTD
)
80 (new preproc MetIDEA
, log2 transform mean centered
)
81 (chromatoplots "our method"))))