Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
RAW Microarray DataDescriptionUnprocessed microarray data stored in an Usagedata(a) FormatFormal class 'AffyBatch' [package "affy"] with 10 slots ..@ cdfName : chr "Mouse430_2" ..@ nrow : Named int 1002 .. ..- attr(*, "names")= chr "Rows" ..@ ncol : Named int 1002 .. ..- attr(*, "names")= chr "Cols" ..@ assayData :<environment: 0xd659090> ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 5 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:5] NA NA NA NA ... .. .. ..@ data :'data.frame': 101 obs. of 5 variables: .. .. .. ..$ File.name : chr [1:101] "1_C32_IN" "2_C32_IN" "3_C32_IN" "4_C32_IN" ... .. .. .. ..$ Embryonic.day : Factor w/ 3 levels "E3.25","E3.5",..: 1 1 1 1 1 1 1 1 1 1 ... .. .. .. ..$ Total.number.of.cells: Factor w/ 11 levels "32","33","34",..: 1 1 1 1 1 1 1 1 1 1 ... .. .. .. ..$ lineage : chr [1:101] "" "" "" "" ... .. .. .. ..$ genotype : Factor w/ 2 levels "FGF4-KO","WT": 2 2 2 2 2 2 2 2 2 2 ... .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ featureData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable: .. .. .. ..$ labelDescription: chr(0) .. .. ..@ data :'data.frame': 1004004 obs. of 0 variables .. .. ..@ dimLabels : chr [1:2] "featureNames" "featureColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ experimentData :Formal class 'MIAME' [package "Biobase"] with 13 slots .. .. ..@ name : chr "" .. .. ..@ lab : chr "" .. .. ..@ contact : chr "" .. .. ..@ title : chr "" .. .. ..@ abstract : chr "" .. .. ..@ url : chr "" .. .. ..@ pubMedIds : chr "" .. .. ..@ samples : list() .. .. ..@ hybridizations : list() .. .. ..@ normControls : list() .. .. ..@ preprocessing :List of 2 .. .. .. ..$ filenames : chr [1:101] "/tmp/RtmpI5T6yy/1_C32_IN.CEL" "/tmp/RtmpI5T6yy/2_C32_IN.CEL" "/tmp/RtmpI5T6yy/3_C32_IN.CEL" "/tmp/RtmpI5T6yy/4_C32_IN.CEL" ... .. .. .. ..$ affyversion: chr NA .. .. ..@ other :List of 1 .. .. .. ..$ : chr "" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 2 .. .. .. .. .. ..$ : int [1:3] 1 0 0 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ annotation : chr "mouse4302" ..@ protocolData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 1 obs. of 1 variable: .. .. .. ..$ labelDescription: chr NA .. .. ..@ data :'data.frame': 101 obs. of 1 variable: .. .. .. ..$ ScanDate: chr [1:101] "2011-03-16T04:33:05Z" "2011-03-16T04:42:32Z" "2011-03-16T04:51:54Z" "2011-03-16T05:19:47Z" ... .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. ..@ .Data:List of 4 .. .. .. ..$ : int [1:3] 3 0 2 .. .. .. ..$ : int [1:3] 2 22 0 .. .. .. ..$ : int [1:3] 1 3 0 .. .. .. ..$ : int [1:3] 1 2 0 ReferencesOhnishi et al., 2014 See Also
Examplesdata(a) a pData(a) Results
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> library(Hiiragi2013)
Loading required package: affy
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: boot
Loading required package: clue
Loading required package: cluster
Loading required package: genefilter
Loading required package: geneplotter
Loading required package: lattice
Attaching package: 'lattice'
The following object is masked from 'package:boot':
melanoma
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: XML
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Loading required package: gtools
Attaching package: 'gtools'
The following objects are masked from 'package:boot':
inv.logit, logit
Loading required package: KEGGREST
Loading required package: MASS
Attaching package: 'MASS'
The following object is masked from 'package:AnnotationDbi':
select
The following object is masked from 'package:genefilter':
area
Loading required package: mouse4302.db
Loading required package: org.Mm.eg.db
Loading required package: RColorBrewer
Loading required package: xtable
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Hiiragi2013/a.Rd_%03d_medium.png", width=480, height=480)
> ### Name: a
> ### Title: RAW Microarray Data
> ### Aliases: a
> ### Keywords: datasets
>
> ### ** Examples
>
> data(a)
> a
AffyBatch object
size of arrays=1002x1002 features (58 kb)
cdf=Mouse430_2 (45101 affyids)
number of samples=101
number of genes=45101
annotation=mouse4302
notes=
Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'mouse4302cdf'
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'mouse4302cdf'
> pData(a)
File.name Embryonic.day Total.number.of.cells lineage
1_C32_IN.CEL 1_C32_IN E3.25 32
2_C32_IN.CEL 2_C32_IN E3.25 32
3_C32_IN.CEL 3_C32_IN E3.25 32
4_C32_IN.CEL 4_C32_IN E3.25 32
5_C32_IN.CEL 5_C32_IN E3.25 32
6_C32_IN.CEL 6_C32_IN E3.25 32
7_C32_IN.CEL 7_C32_IN E3.25 32
8_C32_IN.CEL 8_C32_IN E3.25 32
9_C32_IN.CEL 9_C32_IN E3.25 32
10_C32_IN.CEL 10_C32_IN E3.25 32
11_C32_IN.CEL 11_C32_IN E3.25 32
12_C33_IN.CEL 12_C33_IN E3.25 33
13_C33_IN.CEL 13_C33_IN E3.25 33
14_C33_IN.CEL 14_C33_IN E3.25 33
15_C33_IN.CEL 15_C33_IN E3.25 33
16_C33_IN.CEL 16_C33_IN E3.25 33
17_C33_IN.CEL 17_C33_IN E3.25 33
18_C34_IN.CEL 18_C34_IN E3.25 34
19_C34_IN.CEL 19_C34_IN E3.25 34
20_C34_IN.CEL 20_C34_IN E3.25 34
21_C34_IN.CEL 21_C34_IN E3.25 34
22_C34_IN.CEL 22_C34_IN E3.25 34
23_C41_IN.CEL 23_C41_IN E3.25 41
24_C41_IN.CEL 24_C41_IN E3.25 41
25_C41_IN.CEL 25_C41_IN E3.25 41
26_C41_IN.CEL 26_C41_IN E3.25 41
27_C49_IN.CEL 27_C49_IN E3.25 49
28_C49_IN.CEL 28_C49_IN E3.25 49
29_C49_IN.CEL 29_C49_IN E3.25 49
30_C49_IN.CEL 30_C49_IN E3.25 49
31_C50_IN.CEL 31_C50_IN E3.25 50
32_C50_IN.CEL 32_C50_IN E3.25 50
33_C50_IN.CEL 33_C50_IN E3.25 50
34_C50_IN.CEL 34_C50_IN E3.25 50
35_C50_IN.CEL 35_C50_IN E3.25 50
36_C50_IN.CEL 36_C50_IN E3.25 50
37_C62_PE.CEL 37_C62_PE E3.5 62 PE
38_C62_PE.CEL 38_C62_PE E3.5 62 PE
39_C62_EPI.CEL 39_C62_EPI E3.5 62 EPI
40_C62_EPI.CEL 40_C62_EPI E3.5 62 EPI
41_C62_PE.CEL 41_C62_PE E3.5 62 PE
42_C62_EPI.CEL 42_C62_EPI E3.5 62 EPI
43_C75_PE.CEL 43_C75_PE E3.5 75 PE
44_C75_EPI.CEL 44_C75_EPI E3.5 75 EPI
45_C75_EPI.CEL 45_C75_EPI E3.5 75 EPI
46_C75_EPI.CEL 46_C75_EPI E3.5 75 EPI
47_C75_EPI.CEL 47_C75_EPI E3.5 75 EPI
48_C75_EPI.CEL 48_C75_EPI E3.5 75 EPI
49_C75_PE.CEL 49_C75_PE E3.5 75 PE
50_C75_PE.CEL 50_C75_PE E3.5 75 PE
51_C91_PE.CEL 51_C91_PE E3.5 91 PE
52_C91_PE.CEL 52_C91_PE E3.5 91 PE
53_C91_PE.CEL 53_C91_PE E3.5 91 PE
54_C91_PE.CEL 54_C91_PE E3.5 91 PE
55_C91_EPI.CEL 55_C91_EPI E3.5 91 EPI
56_C91_EPI.CEL 56_C91_EPI E3.5 91 EPI
57_C91_EPI.CEL 57_C91_EPI E3.5 91 EPI
58_C91_PE.CEL 58_C91_PE E3.5 91 PE
59_C207_PE.CEL 59_C207_PE E4.5 207 PE
60_C207_EPI.CEL 60_C207_EPI E4.5 207 EPI
61_C207_PE.CEL 61_C207_PE E4.5 207 PE
62_C207_EPI.CEL 62_C207_EPI E4.5 207 EPI
63_C207_EPI.CEL 63_C207_EPI E4.5 207 EPI
64_C207_EPI.CEL 64_C207_EPI E4.5 207 EPI
65_C207_PE.CEL 65_C207_PE E4.5 207 PE
66_C207_PE.CEL 66_C207_PE E4.5 207 PE
67_e3.25_KO.CEL 67_e3.25_KO E3.25 32 FGF4-KO
68_e3.25_KO.CEL 68_e3.25_KO E3.25 32 FGF4-KO
69_e3.25_KO.CEL 69_e3.25_KO E3.25 32 FGF4-KO
70_e3.25_KO.CEL 70_e3.25_KO E3.25 32 FGF4-KO
71_e3.25_KO.CEL 71_e3.25_KO E3.25 32 FGF4-KO
72_e3.25_KO.CEL 72_e3.25_KO E3.25 32 FGF4-KO
73_e3.25_KO.CEL 73_e3.25_KO E3.25 32 FGF4-KO
74_e3.25_KO.CEL 74_e3.25_KO E3.25 32 FGF4-KO
84_e3.25_KO.CEL 84_e3.25_KO E3.25 <NA> FGF4-KO
85_e3.25_KO.CEL 85_e3.25_KO E3.25 <NA> FGF4-KO
86_e3.25_KO.CEL 86_e3.25_KO E3.25 <NA> FGF4-KO
87_e3.25_KO.CEL 87_e3.25_KO E3.25 <NA> FGF4-KO
88_e3.25_KO.CEL 88_e3.25_KO E3.25 <NA> FGF4-KO
89_e3.25_KO.CEL 89_e3.25_KO E3.25 <NA> FGF4-KO
90_e3.25_KO.CEL 90_e3.25_KO E3.25 <NA> FGF4-KO
91_e3.25_KO.CEL 91_e3.25_KO E3.25 <NA> FGF4-KO
92_e3.25_KO.CEL 92_e3.25_KO E3.25 <NA> FGF4-KO
118_e3.5_KO.CEL 118_e3.5_KO E3.5 <NA> FGF4-KO
119_e3.5_KO.CEL 119_e3.5_KO E3.5 <NA> FGF4-KO
120_e3.5_KO.CEL 120_e3.5_KO E3.5 <NA> FGF4-KO
121_e3.5_KO.CEL 121_e3.5_KO E3.5 <NA> FGF4-KO
122_e3.5_KO.CEL 122_e3.5_KO E3.5 <NA> FGF4-KO
123_e3.5_KO.CEL 123_e3.5_KO E3.5 <NA> FGF4-KO
124_e3.5_KO.CEL 124_e3.5_KO E3.5 <NA> FGF4-KO
125_e3.5_KO.CEL 125_e3.5_KO E3.5 <NA> FGF4-KO
126_e4.5_KO.CEL 126_e4.5_KO E4.5 <NA> FGF4-KO
127_e4.5_KO.CEL 127_e4.5_KO E4.5 <NA> FGF4-KO
128_e4.5_KO.CEL 128_e4.5_KO E4.5 <NA> FGF4-KO
129_e4.5_KO.CEL 129_e4.5_KO E4.5 <NA> FGF4-KO
130_e4.5_KO.CEL 130_e4.5_KO E4.5 <NA> FGF4-KO
131_e4.5_KO.CEL 131_e4.5_KO E4.5 <NA> FGF4-KO
132_e4.5_KO.CEL 132_e4.5_KO E4.5 <NA> FGF4-KO
133_e4.5_KO.CEL 133_e4.5_KO E4.5 <NA> FGF4-KO
134_e4.5_KO.CEL 134_e4.5_KO E4.5 <NA> FGF4-KO
135_e4.5_KO.CEL 135_e4.5_KO E4.5 <NA> FGF4-KO
genotype ScanDate
1_C32_IN.CEL WT 2011-03-16
2_C32_IN.CEL WT 2011-03-16
3_C32_IN.CEL WT 2011-03-16
4_C32_IN.CEL WT 2011-03-16
5_C32_IN.CEL WT 2011-03-16
6_C32_IN.CEL WT 2011-03-16
7_C32_IN.CEL WT 2011-03-16
8_C32_IN.CEL WT 2011-03-16
9_C32_IN.CEL WT 2011-03-16
10_C32_IN.CEL WT 2011-03-16
11_C32_IN.CEL WT 2011-03-16
12_C33_IN.CEL WT 2011-03-15
13_C33_IN.CEL WT 2011-03-15
14_C33_IN.CEL WT 2011-03-15
15_C33_IN.CEL WT 2011-03-15
16_C33_IN.CEL WT 2011-03-15
17_C33_IN.CEL WT 2011-03-15
18_C34_IN.CEL WT 2010-07-02
19_C34_IN.CEL WT 2010-07-02
20_C34_IN.CEL WT 2010-07-02
21_C34_IN.CEL WT 2010-07-02
22_C34_IN.CEL WT 2010-07-02
23_C41_IN.CEL WT 2010-07-02
24_C41_IN.CEL WT 2010-07-02
25_C41_IN.CEL WT 2010-07-02
26_C41_IN.CEL WT 2010-07-02
27_C49_IN.CEL WT 2010-07-02
28_C49_IN.CEL WT 2010-07-02
29_C49_IN.CEL WT 2010-07-02
30_C49_IN.CEL WT 2010-07-02
31_C50_IN.CEL WT 2010-07-02
32_C50_IN.CEL WT 2010-07-02
33_C50_IN.CEL WT 2010-07-02
34_C50_IN.CEL WT 2010-07-02
35_C50_IN.CEL WT 2010-07-02
36_C50_IN.CEL WT 2010-07-02
37_C62_PE.CEL WT 2010-06-30
38_C62_PE.CEL WT 2010-06-30
39_C62_EPI.CEL WT 2010-06-30
40_C62_EPI.CEL WT 2010-06-30
41_C62_PE.CEL WT 2010-07-01
42_C62_EPI.CEL WT 2010-07-01
43_C75_PE.CEL WT 2010-07-01
44_C75_EPI.CEL WT 2010-07-01
45_C75_EPI.CEL WT 2010-07-01
46_C75_EPI.CEL WT 2010-07-01
47_C75_EPI.CEL WT 2010-07-01
48_C75_EPI.CEL WT 2010-07-01
49_C75_PE.CEL WT 2010-07-01
50_C75_PE.CEL WT 2010-07-01
51_C91_PE.CEL WT 2010-09-16
52_C91_PE.CEL WT 2010-09-16
53_C91_PE.CEL WT 2010-09-16
54_C91_PE.CEL WT 2010-09-16
55_C91_EPI.CEL WT 2010-09-16
56_C91_EPI.CEL WT 2010-09-16
57_C91_EPI.CEL WT 2010-09-16
58_C91_PE.CEL WT 2010-09-16
59_C207_PE.CEL WT 2010-07-01
60_C207_EPI.CEL WT 2010-07-01
61_C207_PE.CEL WT 2010-07-01
62_C207_EPI.CEL WT 2010-07-01
63_C207_EPI.CEL WT 2010-07-01
64_C207_EPI.CEL WT 2010-07-01
65_C207_PE.CEL WT 2010-07-02
66_C207_PE.CEL WT 2010-07-02
67_e3.25_KO.CEL FGF4-KO 2012-03-16
68_e3.25_KO.CEL FGF4-KO 2012-03-16
69_e3.25_KO.CEL FGF4-KO 2012-03-16
70_e3.25_KO.CEL FGF4-KO 2012-03-16
71_e3.25_KO.CEL FGF4-KO 2012-03-16
72_e3.25_KO.CEL FGF4-KO 2012-03-16
73_e3.25_KO.CEL FGF4-KO 2012-03-16
74_e3.25_KO.CEL FGF4-KO 2012-03-16
84_e3.25_KO.CEL FGF4-KO 2012-08-16
85_e3.25_KO.CEL FGF4-KO 2012-08-16
86_e3.25_KO.CEL FGF4-KO 2012-08-16
87_e3.25_KO.CEL FGF4-KO 2012-08-16
88_e3.25_KO.CEL FGF4-KO 2012-08-16
89_e3.25_KO.CEL FGF4-KO 2012-08-16
90_e3.25_KO.CEL FGF4-KO 2012-08-16
91_e3.25_KO.CEL FGF4-KO 2012-08-16
92_e3.25_KO.CEL FGF4-KO 2012-08-16
118_e3.5_KO.CEL FGF4-KO 2013-03-05
119_e3.5_KO.CEL FGF4-KO 2013-03-05
120_e3.5_KO.CEL FGF4-KO 2013-03-05
121_e3.5_KO.CEL FGF4-KO 2013-03-05
122_e3.5_KO.CEL FGF4-KO 2013-03-05
123_e3.5_KO.CEL FGF4-KO 2013-03-05
124_e3.5_KO.CEL FGF4-KO 2013-03-05
125_e3.5_KO.CEL FGF4-KO 2013-03-05
126_e4.5_KO.CEL FGF4-KO 2013-03-05
127_e4.5_KO.CEL FGF4-KO 2013-03-05
128_e4.5_KO.CEL FGF4-KO 2013-03-05
129_e4.5_KO.CEL FGF4-KO 2013-03-05
130_e4.5_KO.CEL FGF4-KO 2013-03-05
131_e4.5_KO.CEL FGF4-KO 2013-03-05
132_e4.5_KO.CEL FGF4-KO 2013-03-05
133_e4.5_KO.CEL FGF4-KO 2013-03-05
134_e4.5_KO.CEL FGF4-KO 2013-03-05
135_e4.5_KO.CEL FGF4-KO 2013-03-05
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> dev.off()
null device
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and