estimates.2: estimates.2

In CONFESS: Cell OrderiNg by FluorEScence Signal

Description

Example output from the 2nd run of the spotEstimator function

Usage

data("estimates.2")

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"

Value

example intermediates

CONFESS documentation built on Nov. 8, 2020, 6:05 p.m.