How to: Extract probeset summaries (chip effects) as a multi-dimensional array
Chip effects can be read as an R array by calling:
theta <- extractTheta(ces)
The first dimension is always the units, and the last dimension is always the arrays.
Note that this will load all data in to memory.
Example: HG-U133_Plus_2
ces <- getChipEffectSet(plm)
print(ces)
## ChipEffectSet:
## Name: Affymetrix-HeartBrain
## Tags: RBC,QN,RMA
## Path: plmData/Affymetrix-HeartBrain,RBC,QN,RMA/HG-U133_Plus_2
## Platform: Affymetrix
## Chip type: HG-U133_Plus_2,monocell
## Number of arrays: 3
## Names: heart_A, heart_B, heart_C
## Time period: 2009-08-12 22:21:59 -- 2009-08-12 22:21:59
## Total file size: 1.73MB
## RAM: 0.01MB
## Parameters: (probeModel: chr "pm")
theta <- extractTheta(ces, units=1401:1406)
str(theta)
## num [1:6, 1, 1:3] 50.4 1247.7 83.3 56.9 23.7 ...
## - attr(*, "dimnames")=List of 3
## ..$ : NULL
## ..$ : NULL
## ..$ : chr [1:3] "heart_A" "heart_B" "heart_C"
theta <- extractTheta(ces, units=1401:1406, drop=TRUE)
str(theta)
## num [1:6, 1:3] 50.4 1247.7 83.3 56.9 23.7 ...
## - attr(*, "dimnames")=List of 2
## ..$ : NULL
## ..$ : chr [1:3] "heart_A" "heart_B" "heart_C"
print(theta)
## heart_A heart_B heart_C
## [1,] 50.35944 50.97249 44.04873
## [2,] 1247.74109 1182.60449 1151.22278
## [3,] 83.30342 81.10368 69.86592
## [4,] 56.92453 65.28267 54.34821
## [5,] 23.72381 31.87461 27.95008
## [6,] 343.54056 326.27948 272.80453
Example: HuEx-1_0-st-v2
Illustration: Different number of exons (groups/probesets) per gene
(unit). Each entry is therefore of length equal to the number of exons
(K) of the largest gene holding (theta1, theta2, ..., thetaK) values.
For genes with fewer exons than K, the "missing" entries have all NAs.
ces <- getChipEffectSet(plm)
print(ces)
## ExonChipEffectSet:
## Name: Affymetrix-HeartBrain
## Tags: RBC,QN,RMA
## Path: plmData/Affymetrix-HeartBrain,RBC,QN,RMA/HuEx-1_0-st-v2
## Platform: Affymetrix
## Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP,monocell
## Number of arrays: 3
## Names: cerebellum_A, cerebellum_B, cerebellum_C
## Time period: 2009-10-05 23:54:34 -- 2009-10-05 23:54:34
## Total file size: 8.15MB
## RAM: 0.01MB
## Parameters: (probeModel: chr "pm", mergeGroups: logi FALSE)
theta <- extractTheta(ces, units=101:103)
str(theta)
## num [1:3, 1:9, 1:3] 4.98 9.75 8.09 28.01 126.74 ...
## - attr(*, "dimnames")=List of 3
## ..$ : NULL
## ..$ : NULL
## ..$ : chr [1:3] "cerebellum_A" "cerebellum_B" "cerebellum_C"
print(theta)
## , , cerebellum_A
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
## [1,] 4.9773 28.008 81.885 59.330 11.2939 23.003 NA NA NA
## [2,] 9.7513 126.743 76.986 75.909 39.8756 21.519 69.14 68.302 3.0645
## [3,] 8.0941 45.513 13.254 12.434 6.8943 NA NA NA NA
##
## , , cerebellum_B
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
## [1,] 3.2216 33.484 84.715 78.042 26.5029 20.348 NA NA NA
## [2,] 8.6798 169.581 111.474 77.913 52.8681 38.166 83.859 83.67 8.2662
## [3,] 10.9351 59.455 24.090 15.839 7.3441 NA NA NA NA
##
## , , cerebellum_C
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
## [1,] 4.6035 24.981 90.680 101.175 22.1576 19.260 NA NA NA
## [2,] 8.3373 157.298 79.522 56.661 47.4996 36.600 97.568 80.929 8.9555
## [3,] 10.2943 85.226 11.685 12.425 5.2567 NA NA NA NA
Example: GenomeWideSNP_6
Illustration: Each SNP (unit) has (thetaA, thetaB) groups but each CN probe (unit) has only a theta group. Each entry is therefore of length two (by the longest unit) holding (theta1, theta2) values. For SNPs (theta1, theta2) = (thetaA, thetaB) and for CN probes (theta1, theta2) = (theta, NA).
ces <- getChipEffectSet(plm)
print(ces)
## CnChipEffectSet:
## Name: HapMap270
## Tags: 6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG
## Path:
## plmData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG/GenomeWideSNP_6
## Platform: Affymetrix
## Chip type: GenomeWideSNP_6,Full,monocell
## Number of arrays: 3
## Names: NA06985, NA06991, NA06993
## Time period: 2009-10-17 00:49:05 -- 2009-10-17 00:49:05
## Total file size: 80.85MB
## RAM: 0.01MB
## Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
## combineAlleles: logi FALSE)
theta <- extractTheta(ces, units=c(2101:2104, 935590:935594))
str(theta)
## num [1:9, 1:2, 1:3] 4519 9582 420 769 8724 ...
## - attr(*, "dimnames")=List of 3
## ..\$ : NULL
## ..\$ : NULL
## ..\$ : chr [1:3] "NA06985" "NA06991" "NA06993"
print(theta)
## , , NA06985
## [,1] [,2]
## [1,] 4518.85 522.05
## [2,] 9581.92 503.43
## [3,] 420.19 7162.17
## [4,] 768.96 1117.02
## [5,] 8724.15 NA
## [6,] 7947.55 NA
## [7,] 12863.29 NA
## [8,] 14373.10 NA
## [9,] 23424.00 NA
##
## , , NA06991
## [,1] [,2]
## [1,] 4922.2 522.58
## [2,] 5727.6 2966.96
## [3,] 4732.7 4731.73
## [4,] 1477.6 358.71
## [5,] 7612.3 NA
## [6,] 5970.8 NA
## [7,] 12642.6 NA
## [8,] 11287.0 NA
## [9,] 26139.4 NA
##
## , , NA06993
## [,1] [,2]
## [1,] 5225.9 725.81
## [2,] 1274.1 6061.83
## [3,] 8462.5 207.93
## [4,] 1134.0 419.36
## [5,] 8564.7 NA
## [6,] 6425.6 NA
## [7,] 12712.8 NA
## [8,] 10031.6 NA
## [9,] 17312.8 NA