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R: Class "marrayRaw", classes and methods for pre-normalization...

marrayRaw-class

R Documentation

Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data

Description

This class represents pre-normalization intensity data for a batch of cDNA microarrays. A batch of arrays consists of a collection of arrays with the same layout ("marrayLayout"). The class contains slots for the green (Cy3) and red (Cy5) foreground and background intensities, the layout of the arrays, and descriptions of the target samples hybridized to the arrays and probe sequences spotted onto the arrays.

Objects from the Class

Objects can be created by calls of the form new('marrayRaw',
maRf = ...., # Object of class matrix
maGf = ...., # Object of class matrix
maRb = ...., # Object of class matrix
maGb = ...., # Object of class matrix
maW = ...., # Object of class matrix
maLayout = ...., # Object of class marrayLayout
maGnames = ...., # Object of class marrayInfo
maTargets = ...., # Object of class marrayInfo
maNotes = ...., # Object of class character
)

Slots

maRf:: Object of class "matrix", red foreground intensities, rows correspond to spotted probe sequences, columns to arrays in the batch.
maGf:: Object of class "matrix", green foreground intensities, rows correspond to spotted probe sequences, columns to arrays in the batch.
maRb:: Object of class "matrix", red background intensities, rows correspond to spotted probe sequences, columns to arrays in the batch.
maGb:: Object of class "matrix", green background intensities, rows correspond to spotted probe sequences, columns to arrays in the batch.
maW:: Object of class "matrix", spot quality weights, rows correspond to spotted probe sequences, columns to arrays in the batch.
maLayout:: Object of class "marrayLayout", layout parameters for the cDNA microarrays.
maGnames:: Object of class "marrayInfo", description of spotted probe sequences.
maTargets:: Object of class "marrayInfo", description of target samples hybridized to the arrays.
maNotes:: Object of class "character", any notes concerning the microarray experiments, e.g. hybridization or scanning conditions.

Methods

[: signature(x = "marrayRaw"): subsetting operator for spots on the array and arrays in the batch, ensures that all slots are subset properly.
coerce: signature(from = "marrayRaw", to = "marrayNorm"): coerce an object of class "marrayRaw" into an object of class "marrayNorm".
maA: signature(object = "marrayRaw"): function which computes average log-intensities (base 2) A for an object of class "marrayRaw".
maControls<-: signature(object = "marrayRaw"): slot assignment method.
maControls: signature(object = "marrayRaw"): slot accessor method.
maGb: signature(object = "marrayRaw"): slot accessor method.
maGb<-: signature(object = "marrayRaw", value = "matrix"): slot assignment method.
maGb<-: signature(object = "marrayRaw", value = "NULL"): slot assignment method.
maGf: signature(object = "marrayRaw"): slot accessor method.
maGf<-: signature(object = "marrayRaw", value = "matrix"): slot assignment method.
maGnames: signature(object = "marrayRaw"): slot accessor method.
maGnames<-: signature(object = "marrayRaw", value = "marrayInfo"): slot assignment method.
maGridCol: signature(object = "marrayRaw"): method which computes a vector of grid column coordinates for each spot.
maGridRow: signature(object = "marrayRaw"): method which computes a vector of grid row coordinates for each spot.
maLayout: signature(object = "marrayRaw"): slot accessor method.
maLayout<-: signature(object = "marrayRaw", value = "marrayLayout"): slot assignment method.
maLG: signature(object = "marrayRaw"): method which computes green log-intensities (base 2) for an object of class "marrayRaw".
maLR: signature(object = "marrayRaw"): method which computes red log-intensities (base 2) for an object of class "marrayRaw".
maM: signature(object = "marrayRaw"): method which computes intensity log-ratios (base 2) M for an object of class "marrayRaw".
maNgc: signature(object = "marrayRaw"): slot accessor method.
maNgc<-: signature(object = "marrayRaw", value = "numeric"): slot assignment method.
maNgr: signature(object = "marrayRaw"): slot accessor method.
maNgr<-: signature(object = "marrayRaw", value = "numeric"): slot assignment method.
maNotes: signature(object = "marrayRaw"): slot accessor method.
maNotes<-: signature(object = "marrayRaw", value = "character"): slot assignment method.
maNsamples: signature(object = "marrayRaw"): slot accessor method.
maNsc: signature(object = "marrayRaw"): slot accessor method.
maNsc<-: signature(object = "marrayRaw", value = "numeric"): slot assignment method.
maNspots: signature(object = "marrayRaw"): slot accessor method.
maNspots<-: signature(object = "marrayRaw", value = "numeric"): slot assignment method.
maNsr: signature(object = "marrayRaw"): slot accessor method.
maNsr<-: signature(object = "marrayRaw", value = "numeric"): slot assignment method.
maPlate: signature(object = "marrayRaw"): slot accessor method.
maPlate<-: signature(object = "marrayRaw"): slot assignment method.
maPrintTip: signature(object = "marrayRaw"): method which computes a vector of print-tip-group indices for each spot.
maRb: signature(object = "marrayRaw"): slot accessor method.
maRb<-: signature(object = "marrayRaw", value = "matrix"): slot assignment method.
maRb<-: signature(object = "marrayRaw", value = "NULL"): slot assignment method.
maRf: signature(object = "marrayRaw"): slot accessor method.
maRf<-: signature(object = "marrayRaw", value = "matrix"): slot assignment method.
maSpotCol: signature(object = "marrayRaw"): method which computes a vector of spot column coordinates for each spot.
maSpotRow: signature(object = "marrayRaw"): method which computes a vector of spot row coordinates for each spot.
maSub: signature(object = "marrayRaw"): slot accessor method.
maSub<-: signature(object = "marrayRaw"): slot assignment method.
maTargets: signature(object = "marrayRaw"): slot accessor method.
maTargets<-: signature(object = "marrayRaw", value = "marrayInfo"): slot assignment method.
maW: signature(object = "marrayRaw"): slot accessor method.
maW<-: signature(object = "marrayRaw", value = "matrix"): slot assignment method.
print: signature(x = "marrayRaw"): print method for "marrayRaw" class.

Author(s)

Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine.

References

S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, The Analysis of Gene Expression Data: Methods and Software, Springer, New York.

Examples

# Examples use swirl dataset, for description type ? swirl
require(limma)
data(swirl)

# Object of class marrayRaw for the 4 swirl arrays
swirl

# Object of class marrayLayout
maLayout(swirl)

# Access only the first 100 spots of the third array
swirl[1:100,3]

# Accessor methods -- How many spots on the array
maNspots(swirl)

# Density plot of log-ratios M for third array
plot(density(maM(swirl[,3])))

# Assignment methods -- Replace maNotes slot
maNotes(swirl)
maNotes(swirl)<-"This is a zebrafish microarray"
maNotes(swirl)

Results


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> library(marray)
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/marray/marrayRaw-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: marrayRaw-class
> ### Title: Class "marrayRaw", classes and methods for pre-normalization
> ###   cDNA microarray intensity data
> ### Aliases: marrayRaw-class marrayRaw maRf maRf<- maGf maGf<- maRb maRb<-
> ###   maGb maGb<- maW maW<- maLayout maLayout<- [,marrayRaw-method
> ###   cbind,marrayRaw-method maA,marrayRaw-method
> ###   maControls<-,marrayRaw-method maControls,marrayRaw-method
> ###   maGb<-,marrayRaw,matrix-method maGb<-,marrayRaw,NULL-method
> ###   maGb,marrayRaw-method maGf<-,marrayRaw,matrix-method
> ###   maGf,marrayRaw-method maGnames,marrayRaw-method
> ###   maGridCol,marrayRaw-method maGridRow,marrayRaw-method
> ###   maLayout,marrayRaw-method maLG,marrayRaw-method maLR,marrayRaw-method
> ###   maM,marrayRaw-method maNgc<-,marrayRaw,numeric-method
> ###   maNgc,marrayRaw-method maNgr<-,marrayRaw,numeric-method
> ###   maNgr,marrayRaw-method maNotes<-,marrayRaw,character-method
> ###   maNotes,marrayRaw-method maNsamples,marrayRaw-method
> ###   maNsc<-,marrayRaw,numeric-method maNsc,marrayRaw-method
> ###   maNspots<-,marrayRaw,numeric-method maNspots,marrayRaw-method
> ###   maNsr<-,marrayRaw,numeric-method maNsr,marrayRaw-method
> ###   maPlate<-,marrayRaw-method maPlate,marrayRaw-method
> ###   maPrintTip,marrayRaw-method maRb<-,marrayRaw,matrix-method
> ###   maRb<-,marrayRaw,NULL-method maRb,marrayRaw-method
> ###   maRf<-,marrayRaw,matrix-method maRf,marrayRaw-method
> ###   maSpotCol,marrayRaw-method maSpotRow,marrayRaw-method
> ###   maSub<-,marrayRaw-method maSub,marrayRaw-method
> ###   maTargets,marrayRaw-method maW<-,marrayRaw,matrix-method
> ###   maW,marrayRaw-method print,marrayRaw-method show,marrayRaw-method
> ###   summary,marrayRaw-method maGnames maGnames<- maTargets maTargets<-
> ###   maLR maLG maNsamples
> ### Keywords: classes
> 
> ### ** Examples
> 
> # Examples use swirl dataset, for description type ? swirl
> require(limma)
> data(swirl)
> 
> # Object of class marrayRaw for the 4 swirl arrays
> swirl
An object of class "marrayRaw"
@maRf
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.1.spot
[1,]                                              19538.470
[2,]                                              23619.820
[3,]                                              21579.950
[4,]                                               8905.143
[5,]                                               8676.095
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.2.spot
[1,]                                              16138.720
[2,]                                              17247.670
[3,]                                              17317.150
[4,]                                               6794.381
[5,]                                               6043.542
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.3.spot
[1,]                                              2895.1600
[2,]                                              2976.6230
[3,]                                              2735.6190
[4,]                                               318.9524
[5,]                                               780.6667
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.4.spot
[1,]                                             14054.5400
[2,]                                             20112.2600
[3,]                                             12945.8500
[4,]                                               524.0476
[5,]                                               304.6190
8443 more rows ...

@maGf
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.1.spot
[1,]                                              22028.260
[2,]                                              25613.200
[3,]                                              22652.390
[4,]                                               8929.286
[5,]                                               8746.476
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.2.spot
[1,]                                              19278.770
[2,]                                              21438.960
[3,]                                              20386.470
[4,]                                               6677.619
[5,]                                               6576.292
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.3.spot
[1,]                                              2727.5600
[2,]                                              2787.0330
[3,]                                              2419.8810
[4,]                                               383.2381
[5,]                                               901.0000
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.4.spot
[1,]                                             19930.6500
[2,]                                             25426.5800
[3,]                                             16225.9500
[4,]                                               786.9048
[5,]                                               468.0476
8443 more rows ...

@maRb
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.1.spot
[1,]                                                    174
[2,]                                                    174
[3,]                                                    174
[4,]                                                    163
[5,]                                                    140
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.2.spot
[1,]                                                    136
[2,]                                                    133
[3,]                                                    133
[4,]                                                    105
[5,]                                                    105
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.3.spot
[1,]                                                     82
[2,]                                                     82
[3,]                                                     76
[4,]                                                     61
[5,]                                                     61
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.4.spot
[1,]                                                     48
[2,]                                                     48
[3,]                                                     48
[4,]                                                     48
[5,]                                                     49
8443 more rows ...

@maGb
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.1.spot
[1,]                                                    182
[2,]                                                    171
[3,]                                                    153
[4,]                                                    153
[5,]                                                    153
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.2.spot
[1,]                                                    175
[2,]                                                    183
[3,]                                                    183
[4,]                                                    142
[5,]                                                    142
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.3.spot
[1,]                                                     86
[2,]                                                     86
[3,]                                                     86
[4,]                                                     71
[5,]                                                     71
     C:/GNU/R/R-2.4.1/library/marray/swirldata/swirl.4.spot
[1,]                                                     97
[2,]                                                     85
[3,]                                                     85
[4,]                                                     87
[5,]                                                     87
8443 more rows ...

@maW
<0 x 0 matrix>

@maLayout
An object of class "marrayLayout"
@maNgr
[1] 4

@maNgc
[1] 4

@maNsr
[1] 22

@maNsc
[1] 24

@maNspots
[1] 8448

@maSub
[1] TRUE

@maPlate
factor(0)
Levels: 

@maControls
[1] 1 1 1 1 1
Levels: 0 1
8443 more elements ...

@maNotes
[1] "No Input File"


@maGnames
An object of class "marrayInfo"
@maLabels
[1] "geno1" "geno2" "geno3" "3XSSC" "3XSSC"
8443 more elements ...

@maInfo
     "ID" "Name"
1 control  geno1
2 control  geno2
3 control  geno3
4 control  3XSSC
5 control  3XSSC
8443 more rows ...

@maNotes
[1] "C:/GNU/R/R-2.4.1/library/marray/swirldata/fish.gal"


@maTargets
An object of class "marrayInfo"
@maLabels
[1] "swirl.1.spot" "swirl.2.spot" "swirl.3.spot" "swirl.4.spot"

@maInfo
         Names slide number experiment Cy3 experiment Cy5      date comments
1 swirl.1.spot           81          swirl      wild type 2001/9/20       NA
2 swirl.2.spot           82      wild type          swirl 2001/9/20       NA
3 swirl.3.spot           93          swirl      wild type 2001/11/8       NA
4 swirl.4.spot           94      wild type          swirl 2001/11/8       NA

@maNotes
[1] "C:/GNU/R/R-2.4.1/library/marray/swirldata/SwirlSample.txt"


@maNotes
[1] "Spot Data"

> 
> # Object of class marrayLayout
> maLayout(swirl)
An object of class "marrayLayout"
@maNgr
[1] 4

@maNgc
[1] 4

@maNsr
[1] 22

@maNsc
[1] 24

@maNspots
[1] 8448

@maSub
[1] TRUE

@maPlate
factor(0)
Levels: 

@maControls
[1] 1 1 1 1 1
Levels: 0 1
8443 more elements ...

@maNotes
[1] "No Input File"

> 
> # Access only the first 100 spots of the third array
> swirl[1:100,3]
An object of class "marrayRaw"
@maRf
[1] 2895.1600 2976.6230 2735.6190  318.9524  780.6667
95 more rows ...

@maGf
[1] 2727.5600 2787.0330 2419.8810  383.2381  901.0000
95 more rows ...

@maRb
[1] 82 82 76 61 61
95 more rows ...

@maGb
[1] 86 86 86 71 71
95 more rows ...

@maW
<0 x 0 matrix>

@maLayout
An object of class "marrayLayout"
@maNgr
[1] 4

@maNgc
[1] 4

@maNsr
[1] 22

@maNsc
[1] 24

@maNspots
[1] 8448

@maSub
[1] TRUE TRUE TRUE TRUE TRUE
8443 more elements ...

@maPlate
[1] 1 1 1 1 1
Levels: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
95 more elements ...

@maControls
[1] 1 1 1 1 1
Levels: 0 1
95 more elements ...

@maNotes
[1] "No Input File"


@maGnames
An object of class "marrayInfo"
@maLabels
[1] "geno1" "geno2" "geno3" "3XSSC" "3XSSC"
95 more elements ...

@maInfo
     "ID" "Name"
1 control  geno1
2 control  geno2
3 control  geno3
4 control  3XSSC
5 control  3XSSC
95 more rows ...

@maNotes
[1] "C:/GNU/R/R-2.4.1/library/marray/swirldata/fish.gal"


@maTargets
An object of class "marrayInfo"
@maLabels
[1] "swirl.3.spot"

@maInfo
         Names slide number experiment Cy3 experiment Cy5      date comments
3 swirl.3.spot           93          swirl      wild type 2001/11/8       NA

@maNotes
[1] "C:/GNU/R/R-2.4.1/library/marray/swirldata/SwirlSample.txt"


@maNotes
[1] "Spot Data"

> 
> # Accessor methods -- How many spots on the array
> maNspots(swirl)
[1] 8448
> 
> # Density plot of log-ratios M for third array
> plot(density(maM(swirl[,3])))
> 
> # Assignment methods -- Replace maNotes slot
> maNotes(swirl)
[1] "Spot Data"
> maNotes(swirl)<-"This is a zebrafish microarray"
> maNotes(swirl)
[1] "This is a zebrafish microarray"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>