sizeFactors(sce) samplewise or altogether?

[fulaibaowang]

Hi,

I am following the workshop and have a conceptual question. Should counting size factor should be performed samplewise or on the samples altogether?

Put in another way,

library(MouseGastrulationData)
sce <- WTChimeraData(samples=5:10, type = "processed")
colData(sce)

## DataFrame with 20935 rows and 11 columns
##                   cell          barcode    sample       stage    tomato
##            <character>      <character> <integer> <character> <logical>
## cell_9769    cell_9769 AAACCTGAGACTGTAA         5        E8.5      TRUE
## cell_9770    cell_9770 AAACCTGAGATGCCTT         5        E8.5      TRUE
## cell_9771    cell_9771 AAACCTGAGCAGCCTC         5        E8.5      TRUE
## cell_9772    cell_9772 AAACCTGCATACTCTT         5        E8.5      TRUE
## cell_9773    cell_9773 AAACGGGTCAACACCA         5        E8.5      TRUE
## ...                ...              ...       ...         ...       ...
## cell_30699  cell_30699 TTTGTCACAGCTCGCA        10        E8.5     FALSE
## cell_30700  cell_30700 TTTGTCAGTCTAGTCA        10        E8.5     FALSE
## cell_30701  cell_30701 TTTGTCATCATCGGAT        10        E8.5     FALSE
## cell_30702  cell_30702 TTTGTCATCATTATCC        10        E8.5     FALSE
## cell_30703  cell_30703 TTTGTCATCCCATTTA        10        E8.5     FALSE
##                 pool stage.mapped        celltype.mapped closest.cell
##            <integer>  <character>            <character>  <character>
## cell_9769          3        E8.25             Mesenchyme   cell_24159
## cell_9770          3         E8.5            Endothelium   cell_96660
## cell_9771          3         E8.5              Allantois  cell_134982
## cell_9772          3         E8.5             Erythroid3  cell_133892
## cell_9773          3        E8.25             Erythroid1   cell_76296
## ...              ...          ...                    ...          ...
## cell_30699         5         E8.5             Erythroid3   cell_38810
## cell_30700         5         E8.5       Surface ectoderm   cell_38588
## cell_30701         5        E8.25 Forebrain/Midbrain/H..   cell_66082
## cell_30702         5         E8.5             Erythroid3  cell_138114
## cell_30703         5         E8.0                Doublet   cell_92644
##            doub.density sizeFactor
##               <numeric>  <numeric>
## cell_9769    0.02985045    1.41243
## cell_9770    0.00172753    1.22757
## cell_9771    0.01338013    1.15439
## cell_9772    0.00218402    1.28676
## cell_9773    0.00211723    1.78719
## ...                 ...        ...
## cell_30699   0.00146287   0.389311
## cell_30700   0.00374155   0.588784
## cell_30701   0.05651258   0.624455
## cell_30702   0.00108837   0.550807
## cell_30703   0.82369305   1.184919

How's the sizeFactor calculated, samplewise or altogether?

Many thanks,
y