Format
The format is:
List of 3
$ General :List of 15
..$ index : int [1:246] 1 2 3 4 5 6 7 8 9 10 ...
..$ samples : chr [1:246] "1772-062-248_A01" "1772-062-248_A03" "1772-062-248_A04" "1772-062-248_A06" ...
..$ batch : chr [1:246, 1:2] "1772-062-248" "1772-062-248" "1772-062-248" "1772-062-248" ...
..$ Size : num [1:246] 31 19 152 43 59 21 72 81 31 56 ...
..$ RGexprs :'data.frame': 246 obs. of 4 variables:
.. ..$ fore_Green: num [1:246] 48.4 26.2 45.7 34 24 ...
.. ..$ back_Green: num [1:246] 17.2 17 16.8 17.1 16.8 ...
.. ..$ fore_Red : num [1:246] 219.1 86.5 18.4 84.4 104.3 ...
.. ..$ back_Red : num [1:246] 17.3 17 18 17.7 17.5 ...
..$ exprs : num [1:246, 1:2] 35.3 13.2 32.9 20.9 11.3 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "Green" "Red"
..$ image.type : chr [1:3] "BF" "Green" "Red"
..$ dateIndex : chr "WedMar2313:29:522016"
..$ single.batch.analysis: num 5
..$ BGmethod : chr "normexp"
..$ maxMix : num 3
..$ prior.pi : num 0.1
..$ flex.reps : num 5
..$ flexmethod : chr "BIC"
..$ RNG : NULL
$ Summarized_estimates:List of 3
..$ corrected.exprs : num [1:246, 1:2] 37 11.8 34.4 20.5 9.7 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "Green" "Red"
..$ corrected.transformed.exprs: num [1:246, 1:2] 3.61 2.47 3.54 3.02 2.27 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "Green" "Red"
..$ allResults :List of 2
.. ..$ corrected.exprs : chr [1:247, 1:10] "Ref=1" "40.7543386916705" "13.2747695514339" "37.8669946332554" ...
.. ..$ corrected.transformed.exprs: chr [1:247, 1:10] "Ref=1" "3.70756230498048" "2.58586520738665" "3.63407987867093" ...
$ Batch_estimates :List of 5
..$ Batch1:List of 15
.. ..$ corrected.exprs : num [1:246, 1:2] 40.8 13.3 37.9 22.8 10.8 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ corrected.transformed.exprs : num [1:246, 1:2] 3.71 2.59 3.63 3.13 2.38 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ mixes.Green : num [1:246] 1 1 1 1 1 1 2 1 2 1 ...
.. ..$ mixes.Red : num [1:246] 3 3 1 3 3 3 3 3 3 3 ...
.. ..$ Batch.Green.est : chr [1:11, 1:4] "" "(Intercept)" "factor(Comp)2" "factor(Batch)2" ...
.. ..$ BatchRed.est : chr [1:16, 1:4] "" "(Intercept)" "factor(Comp)2" "factor(Comp)3" ...
.. ..$ fitted.values : num [1:246, 1:2] 2.7 2.7 2.7 2.7 2.7 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ transformation : chr "log"
.. ..$ model.residuals : num [1:246, 1:2] 0.865 -0.114 0.797 0.34 -0.277 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ model.standardized.residuals: num [1:246, 1:2] 1.746 -0.231 1.609 0.687 -0.559 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ residual.statistics : chr [1:4, 1:7] "" "Green" "Red" "Green & Red" ...
.. ..$ lpar : NULL
.. ..$ design.Green : num [1:246, 1:10] 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:246] "1" "2" "3" "4" ...
.. .. .. ..$ : chr [1:10] "(Intercept)" "factor(Comp)2" "factor(Batch)2" "factor(Batch)3" ...
.. .. ..- attr(*, "assign")= int [1:10] 0 1 2 2 2 2 3 3 3 3
.. .. ..- attr(*, "contrasts")=List of 2
.. .. .. ..$ factor(Comp) : chr "contr.treatment"
.. .. .. ..$ factor(Batch): chr "contr.treatment"
.. ..$ design.Red : num [1:246, 1:15] 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:246] "1" "2" "3" "4" ...
.. .. .. ..$ : chr [1:15] "(Intercept)" "factor(Comp)2" "factor(Comp)3" "factor(Batch)2" ...
.. .. ..- attr(*, "assign")= int [1:15] 0 1 1 2 2 2 2 3 3 3 ...
.. .. ..- attr(*, "contrasts")=List of 2
.. .. .. ..$ factor(Comp) : chr "contr.treatment"
.. .. .. ..$ factor(Batch): chr "contr.treatment"
.. ..$ reference : int 1
..$ Batch2:List of 15
.. ..$ corrected.exprs : num [1:246, 1:2] 34.33 9.63 31.69 17.88 8.08 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ corrected.transformed.exprs : num [1:246, 1:2] 3.54 2.26 3.46 2.88 2.09 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ mixes.Green : num [1:246] 1 1 1 1 1 1 1 1 2 1 ...
.. ..$ mixes.Red : num [1:246] 3 3 1 3 3 3 3 3 3 3 ...
.. ..$ Batch.Green.est : chr [1:11, 1:4] "" "(Intercept)" "factor(Comp)2" "factor(Batch)1" ...
.. ..$ BatchRed.est : chr [1:16, 1:4] "" "(Intercept)" "factor(Comp)2" "factor(Comp)3" ...
.. ..$ fitted.values : num [1:246, 1:2] 2.85 2.85 2.85 2.85 2.85 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ transformation : chr "log"
.. ..$ model.residuals : num [1:246, 1:2] 0.717 -0.262 0.649 0.192 -0.425 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ model.standardized.residuals: num [1:246, 1:2] 1.345 -0.492 1.218 0.361 -0.797 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ residual.statistics : chr [1:4, 1:7] "" "Green" "Red" "Green & Red" ...
.. ..$ lpar : NULL
.. ..$ design.Green : num [1:246, 1:10] 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:246] "1" "2" "3" "4" ...
.. .. .. ..$ : chr [1:10] "(Intercept)" "factor(Comp)2" "factor(Batch)1" "factor(Batch)3" ...
.. .. ..- attr(*, "assign")= int [1:10] 0 1 2 2 2 2 3 3 3 3
.. .. ..- attr(*, "contrasts")=List of 2
.. .. .. ..$ factor(Comp) : chr "contr.treatment"
.. .. .. ..$ factor(Batch): chr "contr.treatment"
.. ..$ design.Red : num [1:246, 1:15] 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:246] "1" "2" "3" "4" ...
.. .. .. ..$ : chr [1:15] "(Intercept)" "factor(Comp)2" "factor(Comp)3" "factor(Batch)1" ...
.. .. ..- attr(*, "assign")= int [1:15] 0 1 1 2 2 2 2 3 3 3 ...
.. .. ..- attr(*, "contrasts")=List of 2
.. .. .. ..$ factor(Comp) : chr "contr.treatment"
.. .. .. ..$ factor(Batch): chr "contr.treatment"
.. ..$ reference : int 2
..$ Batch3:List of 15
.. ..$ corrected.exprs : num [1:246, 1:2] 41.7 12.6 38.7 22.7 10.1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ corrected.transformed.exprs : num [1:246, 1:2] 3.73 2.53 3.66 3.12 2.31 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ mixes.Green : num [1:246] 1 1 1 1 1 1 2 1 2 1 ...
.. ..$ mixes.Red : num [1:246] 3 3 1 3 3 3 3 3 3 3 ...
.. ..$ Batch.Green.est : chr [1:11, 1:4] "" "(Intercept)" "factor(Comp)2" "factor(Batch)1" ...
.. ..$ BatchRed.est : chr [1:16, 1:4] "" "(Intercept)" "factor(Comp)2" "factor(Comp)3" ...
.. ..$ fitted.values : num [1:246, 1:2] 2.7 2.7 2.7 2.7 2.7 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ transformation : chr "log"
.. ..$ model.residuals : num [1:246, 1:2] 0.865 -0.114 0.797 0.34 -0.277 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ model.standardized.residuals: num [1:246, 1:2] 1.749 -0.231 1.612 0.688 -0.56 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ residual.statistics : chr [1:4, 1:7] "" "Green" "Red" "Green & Red" ...
.. ..$ lpar : NULL
.. ..$ design.Green : num [1:246, 1:10] 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:246] "1" "2" "3" "4" ...
.. .. .. ..$ : chr [1:10] "(Intercept)" "factor(Comp)2" "factor(Batch)1" "factor(Batch)2" ...
.. .. ..- attr(*, "assign")= int [1:10] 0 1 2 2 2 2 3 3 3 3
.. .. ..- attr(*, "contrasts")=List of 2
.. .. .. ..$ factor(Comp) : chr "contr.treatment"
.. .. .. ..$ factor(Batch): chr "contr.treatment"
.. ..$ design.Red : num [1:246, 1:15] 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:246] "1" "2" "3" "4" ...
.. .. .. ..$ : chr [1:15] "(Intercept)" "factor(Comp)2" "factor(Comp)3" "factor(Batch)1" ...
.. .. ..- attr(*, "assign")= int [1:15] 0 1 1 2 2 2 2 3 3 3 ...
.. .. ..- attr(*, "contrasts")=List of 2
.. .. .. ..$ factor(Comp) : chr "contr.treatment"
.. .. .. ..$ factor(Batch): chr "contr.treatment"
.. ..$ reference : int 3
..$ Batch4:List of 15
.. ..$ corrected.exprs : num [1:246, 1:2] 34.67 11.85 32.27 19.75 9.81 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ corrected.transformed.exprs : num [1:246, 1:2] 3.55 2.47 3.47 2.98 2.28 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ mixes.Green : num [1:246] 1 1 1 1 1 1 2 1 2 1 ...
.. ..$ mixes.Red : num [1:246] 3 3 1 3 3 3 3 3 3 3 ...
.. ..$ Batch.Green.est : chr [1:11, 1:4] "" "(Intercept)" "factor(Comp)2" "factor(Batch)1" ...
.. ..$ BatchRed.est : chr [1:16, 1:4] "" "(Intercept)" "factor(Comp)2" "factor(Comp)3" ...
.. ..$ fitted.values : num [1:246, 1:2] 2.7 2.7 2.7 2.7 2.7 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ transformation : chr "log"
.. ..$ model.residuals : num [1:246, 1:2] 0.865 -0.114 0.797 0.34 -0.277 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ model.standardized.residuals: num [1:246, 1:2] 1.741 -0.23 1.605 0.685 -0.557 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ residual.statistics : chr [1:4, 1:7] "" "Green" "Red" "Green & Red" ...
.. ..$ lpar : NULL
.. ..$ design.Green : num [1:246, 1:10] 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:246] "1" "2" "3" "4" ...
.. .. .. ..$ : chr [1:10] "(Intercept)" "factor(Comp)2" "factor(Batch)1" "factor(Batch)2" ...
.. .. ..- attr(*, "assign")= int [1:10] 0 1 2 2 2 2 3 3 3 3
.. .. ..- attr(*, "contrasts")=List of 2
.. .. .. ..$ factor(Comp) : chr "contr.treatment"
.. .. .. ..$ factor(Batch): chr "contr.treatment"
.. ..$ design.Red : num [1:246, 1:15] 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:246] "1" "2" "3" "4" ...
.. .. .. ..$ : chr [1:15] "(Intercept)" "factor(Comp)2" "factor(Comp)3" "factor(Batch)1" ...
.. .. ..- attr(*, "assign")= int [1:15] 0 1 1 2 2 2 2 3 3 3 ...
.. .. ..- attr(*, "contrasts")=List of 2
.. .. .. ..$ factor(Comp) : chr "contr.treatment"
.. .. .. ..$ factor(Batch): chr "contr.treatment"
.. ..$ reference : int 4
..$ Batch5:List of 17
.. ..$ corrected.exprs : num [1:246, 1:2] 34.3 11.96 31.95 19.7 9.95 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ corrected.transformed.exprs : num [1:246, 1:2] 3.54 2.48 3.46 2.98 2.3 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ mixes.Green : num [1:246] 1 1 1 1 1 1 2 1 2 1 ...
.. ..$ mixes.Red : num [1:246] 2 2 1 2 2 2 2 2 2 2 ...
.. ..$ Batch.Green.est : chr [1:11, 1:4] "" "(Intercept)" "factor(Comp)2" "factor(Batch)1" ...
.. ..$ BatchRed.est : chr [1:11, 1:4] "" "(Intercept)" "factor(Comp)2" "factor(Batch)1" ...
.. ..$ fitted.values : num [1:246, 1:2] 2.7 2.7 2.7 2.7 2.7 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ transformation : chr "log"
.. ..$ model.residuals : num [1:246, 1:2] 0.865 -0.114 0.797 0.34 -0.277 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ model.standardized.residuals: num [1:246, 1:2] 1.749 -0.231 1.612 0.688 -0.56 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : NULL
.. .. .. ..$ : chr [1:2] "Green" "Red"
.. ..$ residual.statistics : chr [1:4, 1:7] "" "Green" "Red" "Green & Red" ...
.. ..$ lpar : NULL
.. ..$ design.Green : num [1:246, 1:10] 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:246] "1" "2" "3" "4" ...
.. .. .. ..$ : chr [1:10] "(Intercept)" "factor(Comp)2" "factor(Batch)1" "factor(Batch)2" ...
.. .. ..- attr(*, "assign")= int [1:10] 0 1 2 2 2 2 3 3 3 3
.. .. ..- attr(*, "contrasts")=List of 2
.. .. .. ..$ factor(Comp) : chr "contr.treatment"
.. .. .. ..$ factor(Batch): chr "contr.treatment"
.. ..$ design.Red : num [1:246, 1:10] 1 1 1 1 1 1 1 1 1 1 ...
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:246] "1" "2" "3" "4" ...
.. .. .. ..$ : chr [1:10] "(Intercept)" "factor(Comp)2" "factor(Batch)1" "factor(Batch)2" ...
.. .. ..- attr(*, "assign")= int [1:10] 0 1 2 2 2 2 3 3 3 3
.. .. ..- attr(*, "contrasts")=List of 2
.. .. .. ..$ factor(Comp) : chr "contr.treatment"
.. .. .. ..$ factor(Batch): chr "contr.treatment"
.. ..$ reference : int 5
.. ..$ Green.contrasts : chr [1:21, 1:7] "Channel" "CH1" "CH1" "CH1" ...
.. ..$ Red.contrasts : chr [1:21, 1:7] "Channel" "CH2" "CH2" "CH2" ...