step2: step2

In CONFESS: Cell OrderiNg by FluorEScence Signal

Description

Example output of the Fluo_adjustment function

Usage

data("step2")

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" ...

Value

example intermediates

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