Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
qPCR Gene ExpressionDescriptionAn Usagedata(xq) FormatFormal class 'ExpressionSet' [package "Biobase"] with 7 slots ..@ 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() .. .. ..@ other : list() .. .. ..@ .__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 ..@ assayData :<environment: 0xb12e938> ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 4 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:4] NA NA NA NA .. .. ..@ data :'data.frame': 137 obs. of 4 variables: .. .. .. ..$ Sample.ID : chr [1:137] "34c_2" "34c_3" "34c_4" "34c_5" ... .. .. .. ..$ Embryonic.day: chr [1:137] "E3.25" "E3.25" "E3.25" "E3.25" ... .. .. .. ..$ Cell.type : chr [1:137] "ICM" "ICM" "ICM" "ICM" ... .. .. .. ..$ sampleGroup : chr [1:137] "E3.25" "E3.25" "E3.25" "E3.25" ... .. .. ..@ 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': 1 obs. of 1 variable: .. .. .. ..$ labelDescription: chr NA .. .. ..@ data :'data.frame': 38 obs. of 1 variable: .. .. .. ..$ symbol: chr [1:38] "Fgf4" "Tom1l1" "Tdgf1" "Cldn4" ... .. .. ..@ 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 ..@ annotation : chr "single cell qPCR" ..@ protocolData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable: .. .. .. ..$ labelDescription: chr(0) .. .. ..@ data :'data.frame': 137 obs. of 0 variables .. .. ..@ 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] 2 15 0 .. .. .. ..$ : int [1:3] 2 16 0 .. .. .. ..$ : int [1:3] 1 3 0 .. .. .. ..$ : int [1:3] 1 0 0 ReferencesOhnishi et al., 2014 See Also
Examplesdata(xq) xq pData(xq) 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/xq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: xq
> ### Title: qPCR Gene Expression
> ### Aliases: xq
> ### Keywords: datasets
>
> ### ** Examples
>
> data(xq)
> xq
ExpressionSet (storageMode: lockedEnvironment)
assayData: 38 features, 137 samples
element names: exprs
protocolData: none
phenoData
sampleNames: 1 E3.25 2 E3.25 ... 137 E4.5 (EPI) (137 total)
varLabels: Sample.ID Embryonic.day Cell.type sampleGroup
varMetadata: labelDescription
featureData
featureNames: Fgf4 Tom1l1 ... Serpine2 (38 total)
fvarLabels: symbol
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: single cell qPCR
> pData(xq)
Sample.ID Embryonic.day Cell.type sampleGroup
1 E3.25 34c_2 E3.25 ICM E3.25
2 E3.25 34c_3 E3.25 ICM E3.25
3 E3.25 34c_4 E3.25 ICM E3.25
4 E3.25 34c_5 E3.25 ICM E3.25
5 E3.25 34c_6 E3.25 ICM E3.25
6 E3.25 34c_7 E3.25 ICM E3.25
7 E3.25 34c_8 E3.25 ICM E3.25
8 E3.25 41c_1 E3.25 ICM E3.25
9 E3.25 41c_3 E3.25 ICM E3.25
10 E3.25 41c_4 E3.25 ICM E3.25
11 E3.25 41c_5 E3.25 ICM E3.25
12 E3.25 41c_6 E3.25 ICM E3.25
13 E3.25 41c_7 E3.25 ICM E3.25
14 E3.25 41c_8 E3.25 ICM E3.25
15 E3.25 49c_1 E3.25 ICM E3.25
16 E3.25 49c_2 E3.25 ICM E3.25
17 E3.25 49c_3 E3.25 ICM E3.25
18 E3.25 49c_4 E3.25 ICM E3.25
19 E3.25 49c_5 E3.25 ICM E3.25
20 E3.25 49c_6 E3.25 ICM E3.25
21 E3.25 49c_7 E3.25 ICM E3.25
22 E3.25 49c_8 E3.25 ICM E3.25
23 E3.25 49c_9 E3.25 ICM E3.25
24 E3.25 50c_13 E3.25 ICM E3.25
25 E3.25 50c_14 E3.25 ICM E3.25
26 E3.25 50c_15 E3.25 ICM E3.25
27 E3.25 50c_16 E3.25 ICM E3.25
28 E3.25 50c_17 E3.25 ICM E3.25
29 E3.25 50c_18 E3.25 ICM E3.25
30 E3.25 50c_19 E3.25 ICM E3.25
31 E3.25 50c_20 E3.25 ICM E3.25
32 E3.25 50c_21 E3.25 ICM E3.25
33 E3.25 50c_22 E3.25 ICM E3.25
34 E3.5 (EPI) 62c_2 E3.5 EPI E3.5 (EPI)
35 E3.5 (EPI) 62c_3 E3.5 EPI E3.5 (EPI)
36 E3.5 (PE) 62c_4 E3.5 PE E3.5 (PE)
37 E3.5 (PE) 62c_5 E3.5 PE E3.5 (PE)
38 E3.5 (PE) 62c_6 E3.5 PE E3.5 (PE)
39 E3.5 (EPI) 62c_9 E3.5 EPI E3.5 (EPI)
40 E3.5 (PE) 62c_10 E3.5 PE E3.5 (PE)
41 E3.5 (EPI) 62c_11 E3.5 EPI E3.5 (EPI)
42 E3.5 (PE) 62c_13 E3.5 PE E3.5 (PE)
43 E3.5 (EPI) 62c_14 E3.5 EPI E3.5 (EPI)
44 E3.5 (PE) 75c_1 E3.5 PE E3.5 (PE)
45 E3.5 (PE) 75c_2 E3.5 PE E3.5 (PE)
46 E3.5 (PE) 75c_3 E3.5 PE E3.5 (PE)
47 E3.5 (EPI) 75c_4 E3.5 EPI E3.5 (EPI)
48 E3.5 (EPI) 75c_5 E3.5 EPI E3.5 (EPI)
49 E3.5 (PE) 75c_6 E3.5 PE E3.5 (PE)
50 E3.5 (EPI) 75c_8 E3.5 EPI E3.5 (EPI)
51 E3.5 (EPI) 75c_9 E3.5 EPI E3.5 (EPI)
52 E3.5 (EPI) 75c_10 E3.5 EPI E3.5 (EPI)
53 E3.5 (EPI) 75c_11 E3.5 EPI E3.5 (EPI)
54 E3.5 (EPI) 75c_12 E3.5 EPI E3.5 (EPI)
55 E3.5 (PE) 75c_13 E3.5 PE E3.5 (PE)
56 E3.5 (EPI) 75c_14 E3.5 EPI E3.5 (EPI)
57 E3.5 (EPI) 75c_15 E3.5 EPI E3.5 (EPI)
58 E3.5 (PE) 75c_16 E3.5 PE E3.5 (PE)
59 E3.5 (EPI) 75c_17 E3.5 EPI E3.5 (EPI)
60 E3.5 (EPI) 75c_18 E3.5 EPI E3.5 (EPI)
61 E3.5 (PE) 75c_19 E3.5 PE E3.5 (PE)
62 E3.5 (PE) 75c_20 E3.5 PE E3.5 (PE)
63 E3.5 (PE) 91c_1 E3.5 PE E3.5 (PE)
64 E3.5 (PE) 91c_2 E3.5 PE E3.5 (PE)
65 E3.5 (PE) 91c_3 E3.5 PE E3.5 (PE)
66 E3.5 (PE) 91c_4 E3.5 PE E3.5 (PE)
67 E3.5 (EPI) 91c_5 E3.5 EPI E3.5 (EPI)
68 E3.5 (PE) 91c_6 E3.5 PE E3.5 (PE)
69 E3.5 (EPI) 91c_8 E3.5 EPI E3.5 (EPI)
70 E3.5 (PE) 91c_9 E3.5 PE E3.5 (PE)
71 E3.5 (EPI) 91c_10 E3.5 EPI E3.5 (EPI)
72 E3.5 (PE) 91c_12 E3.5 PE E3.5 (PE)
73 E3.5 (EPI) 91c_13 E3.5 EPI E3.5 (EPI)
74 E3.5 (EPI) 91c_14 E3.5 EPI E3.5 (EPI)
75 E3.5 (PE) 91c_15 E3.5 PE E3.5 (PE)
76 E3.5 (PE) 91c_16 E3.5 PE E3.5 (PE)
77 E4.5 (EPI) 163c_1 E4.5 EPI E4.5 (EPI)
78 E4.5 (EPI) 163c_2 E4.5 EPI E4.5 (EPI)
79 E4.5 (EPI) 163c_3 E4.5 EPI E4.5 (EPI)
80 E4.5 (EPI) 163c_4 E4.5 EPI E4.5 (EPI)
81 E4.5 (EPI) 163c_5 E4.5 EPI E4.5 (EPI)
82 E4.5 (EPI) 163c_6 E4.5 EPI E4.5 (EPI)
83 E4.5 (PE) 163c_7 E4.5 PE E4.5 (PE)
84 E4.5 (PE) 163c_8 E4.5 PE E4.5 (PE)
85 E4.5 (PE) 163c_9 E4.5 PE E4.5 (PE)
86 E4.5 (PE) 163c_10 E4.5 PE E4.5 (PE)
87 E4.5 (PE) 163c_11 E4.5 PE E4.5 (PE)
88 E4.5 (PE) 163c_12 E4.5 PE E4.5 (PE)
89 E4.5 (EPI) 163c_13 E4.5 EPI E4.5 (EPI)
90 E4.5 (PE) 163c_15 E4.5 PE E4.5 (PE)
91 E4.5 (PE) 163c_16 E4.5 PE E4.5 (PE)
92 E4.5 (PE) 163c_17 E4.5 PE E4.5 (PE)
93 E4.5 (PE) 163c_18 E4.5 PE E4.5 (PE)
94 E4.5 (PE) 163c_19 E4.5 PE E4.5 (PE)
95 E4.5 (PE) 163c_20 E4.5 PE E4.5 (PE)
96 E4.5 (PE) 163c_21 E4.5 PE E4.5 (PE)
97 E4.5 (PE) 207c_1 E4.5 PE E4.5 (PE)
98 E4.5 (EPI) 207c_2 E4.5 EPI E4.5 (EPI)
99 E4.5 (PE) 207c_3 E4.5 PE E4.5 (PE)
100 E4.5 (PE) 207c_4 E4.5 PE E4.5 (PE)
101 E4.5 (EPI) 207c_5 E4.5 EPI E4.5 (EPI)
102 E4.5 (EPI) 207c_6 E4.5 EPI E4.5 (EPI)
103 E4.5 (PE) 207c_7 E4.5 PE E4.5 (PE)
104 E4.5 (PE) 207c_8 E4.5 PE E4.5 (PE)
105 E4.5 (EPI) 207c_10 E4.5 EPI E4.5 (EPI)
106 E4.5 (EPI) 207c_11 E4.5 EPI E4.5 (EPI)
107 E4.5 (EPI) 207c_12 E4.5 EPI E4.5 (EPI)
108 E4.5 (EPI) 207c_13 E4.5 EPI E4.5 (EPI)
109 E4.5 (EPI) 207c_14 E4.5 EPI E4.5 (EPI)
110 E4.5 (PE) 207c_15 E4.5 PE E4.5 (PE)
111 E4.5 (PE) 207c_16 E4.5 PE E4.5 (PE)
112 E4.5 (PE) 207c_17 E4.5 PE E4.5 (PE)
113 E4.5 (PE) 207c_18 E4.5 PE E4.5 (PE)
114 E4.5 (PE) 207c_19 E4.5 PE E4.5 (PE)
115 E4.5 (PE) 207c_20 E4.5 PE E4.5 (PE)
116 E4.5 (PE) 207c_21 E4.5 PE E4.5 (PE)
117 E4.5 (PE) 207c_22 E4.5 PE E4.5 (PE)
118 E4.5 (PE) 227c_2 E4.5 PE E4.5 (PE)
119 E4.5 (PE) 227c_3 E4.5 PE E4.5 (PE)
120 E4.5 (PE) 227c_4 E4.5 PE E4.5 (PE)
121 E4.5 (PE) 227c_5 E4.5 PE E4.5 (PE)
122 E4.5 (EPI) 227c_6 E4.5 EPI E4.5 (EPI)
123 E4.5 (EPI) 227c_7 E4.5 EPI E4.5 (EPI)
124 E4.5 (EPI) 227c_8 E4.5 EPI E4.5 (EPI)
125 E4.5 (EPI) 227c_9 E4.5 EPI E4.5 (EPI)
126 E4.5 (EPI) 227c_10 E4.5 EPI E4.5 (EPI)
127 E4.5 (EPI) 227c_11 E4.5 EPI E4.5 (EPI)
128 E4.5 (EPI) 227c_12 E4.5 EPI E4.5 (EPI)
129 E4.5 (EPI) 227c_13 E4.5 EPI E4.5 (EPI)
130 E4.5 (EPI) 227c_14 E4.5 EPI E4.5 (EPI)
131 E4.5 (EPI) 227c_15 E4.5 EPI E4.5 (EPI)
132 E4.5 (EPI) 227c_16 E4.5 EPI E4.5 (EPI)
133 E4.5 (EPI) 227c_17 E4.5 EPI E4.5 (EPI)
134 E4.5 (EPI) 227c_18 E4.5 EPI E4.5 (EPI)
135 E4.5 (PE) 227c_19 E4.5 PE E4.5 (PE)
136 E4.5 (EPI) 227c_20 E4.5 EPI E4.5 (EPI)
137 E4.5 (EPI) 227c_21 E4.5 EPI E4.5 (EPI)
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