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gradient.norm

Examples of array-CGH data with spatial artifacts

Bundled with MANOR · exported, loads via data()

Class
arrayCGH
Elements
7
Missing
0
Format
rda · xz
version 2 · 277 KB
File
data/spatial.RData
Fingerprint
a295e404
Format documented
Yes
Source
Institut Curie, manor@curie.fr.
Structure
Distinct
7
Nesting depth
2
Element length
1 – 13
Total length
37
Nested rows
14,157
Nested columns
13
Nested schema
varies between elements
Elements
Element
Type
Distinct
Missing
Summary
arrayValues
list
13
0
nested·10,800 rows nested
Element length
10,800 – 10,800
Total length
140,400
Nested rows
10,800
What is inside it
Element
Type
Distinct
Missing
Summary
ChromosomeArm
character
44
768
2 – 3 characters
Col
numeric
60
0
1 – 60mean 30.5
Min.
1
1st Qu.
15.75
Median
30.5
Mean
30.5
3rd Qu.
45.25
Max.
60
Std. dev
17.3189
Skewness
3.126e-14
Kurtosis
-1.201
Row
numeric
180
0
1 – 180mean 90.5
Min.
1
1st Qu.
45.75
Median
90.5
Mean
90.5
3rd Qu.
135.25
Max.
180
Std. dev
51.9631
Skewness
9.745e-15
Kurtosis
-1.2
Clone
integer
3,340
768
1 – 7643mean 2516
Min.
1
1st Qu.
1790.75
Median
2648.5
Mean
2515.82
3rd Qu.
3519.25
Max.
7643
Std. dev
1361.08
Skewness
-0.0656
Kurtosis
0.1901
Outliers
690 low · 69 high
Longest gap
768
Trailing
768
FLAG
integer
2
768
-50 – 0mean -0.309
Min.
-50
1st Qu.
0
Median
0
Mean
-0.309
3rd Qu.
0
Max.
0
Std. dev
3.9188
Skewness
-12.6
Kurtosis
156.8
Zeros
9,970
Longest gap
768
Trailing
768
B2
numeric
319
768
8.022 – 11.414mean 8.434
Min.
8.022
1st Qu.
8.349
Median
8.409
Mean
8.4344
3rd Qu.
8.48
Max.
11.414
Std. dev
0.1947
Skewness
5.615
Kurtosis
60.13
Outliers
896290 low · 606 high
Longest gap
768
Trailing
768
F2
numeric
2,386
768
7.983 – 14.499mean 11.4
Min.
7.983
1st Qu.
11.067
Median
11.413
Mean
11.3991
3rd Qu.
11.761
Max.
14.499
Std. dev
0.5618
Skewness
-0.4253
Kurtosis
2.544
Outliers
204122 low · 82 high
Longest gap
768
Trailing
768
LogRatio
numeric
2,366
780
-4.467 – 4.329·12 NaN
Min.
-4.467
1st Qu.
-0.638
Median
-0.263
Mean
-0.3176
3rd Qu.
0.071
Max.
4.329
Std. dev
0.5628
Skewness
-0.4596
Kurtosis
2.918
Zeros
6
Outliers
171141 low · 30 high
NaN
12of the missing
Longest gap
768
Trailing
768
Chromosome
character
24
768
1 – 2 characters
LogRatioNorm
numeric
1,125
1,584
-4.052 – 2.697·6 NaN
Min.
-4.052
1st Qu.
-0.096
Median
0.009
Mean
0.0248
3rd Qu.
0.135
Max.
2.697
Std. dev
0.2412
Skewness
-2.268
Kurtosis
47.11
Zeros
23
Outliers
31094 low · 216 high
NaN
6of the missing
Longest gap
768
Leading
1
Trailing
768
Flag
character
5
0
1 – 2 characters
FlagT
character
3
0
0 – 1 characters·10,371 blank
Trend
numeric
2,022
0
-1.654 – 0.738mean -0.0789
Min.
-1.654
1st Qu.
-0.37
Median
-0.004
Mean
-0.0789
3rd Qu.
0.255
Max.
0.738
Std. dev
0.4865
Skewness
-0.6098
Kurtosis
-0.1194
Zeros
7
Outliers
135135 low · 0 high
arrayDesign
numeric
3
0
4 – 15mean 11.5
Min.
4
1st Qu.
10
Median
13.5
Mean
11.5
3rd Qu.
15
Max.
15
Std. dev
5.1962
Skewness
-0.5987
Kurtosis
-1.812
Order
ascending
cloneValues
list
11
0
nested·3,340 rows nested
Element length
3,340 – 3,340
Total length
36,740
Nested rows
3,340
What is inside it
Element
Type
Distinct
Missing
Summary
Clone
integer
3,340
0
1 – 7643mean 2513
Min.
1
1st Qu.
1789.75
Median
2648.5
Mean
2513.15
3rd Qu.
3518.25
Max.
7643
Std. dev
1356.15
Skewness
-0.0927
Kurtosis
0.118
Outliers
210 low · 21 high
Chromosome
factor
24
0
1476226552031220031924170+18 more
Levels
24
Used
24
Rows per level
1476226552031220031924170171636157111511014181339128X1277124209513941488158818811679227719482147Y13
Position
integer
3,331
0
8094 – 245273343mean 7.35e+7
Min.
8094
1st Qu.
2.80488e+7
Median
59661519
Mean
7.34976e+7
3rd Qu.
1.10558e+8
Max.
245273343
Std. dev
5.55506e+7
Skewness
0.8274
Kurtosis
-0.0559
Outliers
190 low · 19 high
Validation
integer
7
0
0 – 10mean 4.996
Min.
0
1st Qu.
5
Median
5
Mean
4.9964
3rd Qu.
5
Max.
10
Std. dev
1.3091
Skewness
1.293
Kurtosis
10.51
Zeros
63
LogRatio
numeric
792
113
-3.256 – 2.566·113 NaN
Min.
-3.256
1st Qu.
-0.091
Median
0.008
Mean
0.0255
3rd Qu.
0.1255
Max.
2.566
Std. dev
0.2309
Skewness
-2.131
Kurtosis
44.57
Zeros
9
Outliers
11733 low · 84 high
NaN
113of the missing
Longest gap
2
FlagAgr
character
11
0
1 – 3 characters
FlagT
character
3
0
0 – 3 characters·3,197 blank
Chromosome.num
numeric
24
0
1 – 24mean 9.212
Min.
1
1st Qu.
3
Median
8
Mean
9.2117
3rd Qu.
14
Max.
24
Std. dev
6.7896
Skewness
0.4937
Kurtosis
-0.9273
Order
ascending
PosOrder
integer
3,340
0
1 – 3340mean 1670
Min.
1
1st Qu.
835.75
Median
1670.5
Mean
1670.5
3rd Qu.
2505.25
Max.
3340
Std. dev
964.319
Skewness
-9.919e-17
Kurtosis
-1.201
Order
ascending
LimitChr
numeric
2
0
0 – 1mean 0.0069
Min.
0
1st Qu.
0
Median
0
Mean
0.0069
3rd Qu.
0
Max.
1
Std. dev
0.0827
Skewness
11.92
Kurtosis
140.1
Zeros
3,317
ZoneGNL
factor
4
113
02,6191452-115125
id.rep
character
1
0
5 characters
flags
list
4
0
nested·9 rows nested
Element length
9 – 9
Total length
36
Nested rows
9
What is inside it
Element
Type
Distinct
Missing
Summary
char
factor
9
0
A1B1E1G1OK1P1+3 more
Levels
9
Used
9
Rows per level
A1B1E1G1OK1P1S1U1V1
label
character
9
0
7 – 26 characters
arg
numeric
4
5
0.1 – 3mean 1.525
Min.
0.1
1st Qu.
0.775
Median
1.5
Mean
1.525
3rd Qu.
2.25
Max.
3
Std. dev
1.2527
Skewness
0.0353
Kurtosis
-2.088
Order
descending
Longest gap
2
Leading
2
Trailing
1
count
numeric
6
0
0 – 9990mean 1200
Min.
0
1st Qu.
0
Median
1
Mean
1200
3rd Qu.
204
Max.
9990
Std. dev
3301.16
Skewness
2.062
Kurtosis
2.598
Zeros
4
Outliers
20 low · 2 high
norm.coef
numeric
1
0
-0.2794
quality
list
3
0
nested·8 rows nested
Element length
8 – 8
Total length
24
Nested rows
8
What is inside it
Element
Type
Distinct
Missing
Summary
name
factor
8
0
ANALYSED_CLONES1DYN_X1DYN_Y1LOCAL_SMOOTHNESS1PERCENT_ANALYSED_CLONES1PERCENT_ANALYSED_SPOTS1+2 more
Levels
8
Used
8
Rows per level
ANALYSED_CLONES1DYN_X1DYN_Y1LOCAL_SMOOTHNESS1PERCENT_ANALYSED_CLONES1PERCENT_ANALYSED_SPOTS1PERCENT_REPLICATES1VAR_REPLICATE1
label
factor
8
0
Average proportion of remaining spots by clone after normalization1Average variability among replicates1Local signal variability along the genome1Number of clones after normalization1Proportion of clones after normalization1Proportion of spots after normalization1+2 more
Levels
8
Used
8
Rows per level
Average proportion of remaining spots by clone after normalization1Average variability among replicates1Local signal variability along the genome1Number of clones after normalization1Proportion of clones after normalization1Proportion of spots after normalization1Signal dynamics on X chromosome1Signal dynamics on Y chromosome1
score
numeric
8
0
0.033 – 3227mean 437.8
Min.
0.033
1st Qu.
0.2585
Median
43.2665
Mean
437.805
3rd Qu.
93.075
Max.
3227
Std. dev
1127.91
Skewness
1.85
Kurtosis
1.689
Outliers
10 low · 1 high

The nested tables do not share one set of columns, so there is no single schema to show.

Version history
VersionReleasedSizeChangeStored asConfidence
3.232026-04-287 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.222025-10-297 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.212025-04-157 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.202024-10-297 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.192024-04-307 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.182023-10-247 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.172023-04-257 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.162022-11-017 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.152022-04-267 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.142021-10-267 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.132021-05-197 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.122020-10-277 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.112020-04-277 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.102019-10-297 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.92019-05-027 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.82018-10-307 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.72018-05-117 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.62017-10-307 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.52017-04-247 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.42016-10-177 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.32016-05-037 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.22015-10-137 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.12015-04-167 elementsUnchangedrda · xz
version 2 · 277 KB
exact
3.02014-10-137 elementsUnchangedrda · xz
version 2 · 277 KB
exact
2.142014-04-117 elementsUnchangedrda · xz
version 2 · 277 KB
exact
2.132013-10-147 elementsUnchangedrda · xz
version 2 · 277 KB
exact
2.122013-04-037 elementsUnchangedrda · xz
version 2 · 277 KB
exact
2.112012-10-017 elementsUnchangedrda · xz
version 2 · 277 KB
exact
2.102012-03-307 elementsRepackagedrda · xz
version 2 · 277 KB
exact
2.92011-10-317 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
2.82011-04-147 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
2.72010-10-187 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
2.62010-05-267 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
2.52009-10-277 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
2.42009-04-207 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
2.32008-10-217 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
2.22008-04-307 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
2.12007-10-037 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
2.02007-04-247 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
1.92006-12-157 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
1.82006-04-257 elementsUnchangedrda · gzip
version 2 · 645 KB
exact
1.72005-10-127 elements–rda · gzip
version 2 · 645 KB
exact

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