Description
Example output from the 2nd run of the spotEstimator function
Value
example intermediates
Format
The format is:
List of 6
$ SpotResults :'data.frame': 14 obs. of 15 variables:
..$ SampleID : chr [1:14] "1772-062-248_A01" "1772-062-248_A02" "1772-062-248_A03" "1772-062-248_A04" ...
..$ X : num [1:14] 259 261 262 261 261 258 259 189 195 194 ...
..$ Y : num [1:14] 367 335 368 369 335 367 336 278 250 284 ...
..$ Size : num [1:14] 31 49 19 152 141 43 59 15 49 32 ...
..$ Estimation.Type: chr [1:14] "Fluorescence-based" "Chip.Pattern-based" "Fluorescence-based" "Fluorescence-based" ...
..$ fore_Green : num [1:14] 48.4 18.4 26.2 45.7 32.6 ...
..$ back_Green : num [1:14] 17.2 16.8 16.6 16.9 17.1 ...
..$ fore_Red : num [1:14] 219.1 19.8 86.5 18.4 48 ...
..$ back_Red : num [1:14] 17.5 17.8 17.5 18.1 18 ...
..$ Green.StN : num [1:14] 1.442 0.118 0.626 1.389 0.889 ...
..$ Green.Pvalue : num [1:14] 6.03e-07 1.00 5.55e-02 5.16e-27 4.57e-23 ...
..$ Red.StN : num [1:14] 3.5689 0.1416 2.2422 0.0256 1.3664 ...
..$ Red.Pvalue : num [1:14] 6.16e-07 1.00 7.13e-05 1.00 3.33e-25 ...
..$ Other.Spots : chr [1:14] "0" "0" "X = 30, Y = 204 (Green) | X = 262, Y = 368 (Red)" "0" ...
..$ QCgroup : chr [1:14] "confidence" "contamination" "confidence" "confidence" ...
$ Outlier.Estimates:List of 14
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A01"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A02"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A03"
.. ..$ centerR: num [1:2] 263 370
.. ..$ centerG: num [1:2] 263 370
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : chr "BF"
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A04"
.. ..$ centerR: num [1:2] 265 370
.. ..$ centerG: num [1:2] 265 370
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : chr "BF"
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A05"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A06"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A07"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A01"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A02"
.. ..$ centerR: num [1:2] 195 250
.. ..$ centerG: num [1:2] 195 250
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : chr "BF"
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A03"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A04"
.. ..$ centerR: num [1:2] 191 281
.. ..$ centerG: num [1:2] 191 281
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : chr "BF"
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A05"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A06"
.. ..$ centerR: num [1:2] 187 274
.. ..$ centerG: num [1:2] 187 274
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : chr "BF"
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A07"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
$ Processed.Files :List of 6
..$ BF : chr [1:2] "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/BF/1772-062-248_A02_BF.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/BF/1772-067-039_A02_BF.txt"
..$ CH1 : chr [1:2] "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A02_Green.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-067-039_A02_Green.txt"
..$ CH2 : chr [1:2] "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A02_Red.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-067-039_A02_Red.txt"
..$ separator : chr "_"
..$ image.type: chr [1:3] "BF" "Green" "Red"
..$ dateIndex : chr "WedApr611:21:282016"
$ BFarea : num 7
$ image.type : chr [1:3] "BF" "Green" "Red"
$ dateIndex : chr "WedApr611:21:282016"