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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