I can understand two-color and one-color(Channel) gene chip; but there is another type of gene-Chip called "N-channel chips" ; I do not know how can several (> 2) samples be hybridize in one chip. I cannot find some reference for the a material for this concept. See the following code that it has two channels "E“ and "Eb"; what does that channel mean? The expression matrices seem to have the same dimension. In my understanding, the two-color or two-channel microarray is to combine two samples (treated vs. control) in a chip, and the log(ratio) is used to express the differential expression.
AE1548 = getAE("E-MTAB-1548",
path="/Users/zhang/Documents/2020/GEOsepsis/Data",
local = TRUE, sourcedir = "/Users/zhang/Documents/2020/GEOsepsis/Data",
type = 'full')
AE1548raw = ae2bioc(mageFiles = AE1548)#established from raw data; multi-channel data
AE1548expr1 = assayDataElement(AE1548raw,"E")
AE1548expr2 = assayDataElement(AE1548raw,"Eb")
AE1548expr1[1:5,1:3]
SIRS_18exp2 SIRS_19exp2 SIRS_23exp1
1 273812.0 97733.5 205330
2 41.0 26.5 50
3 42.5 25.0 48
4 40.0 23.5 49
5 38.5 24.0 53
AE1548expr2[1:5,1:3]
SIRS_18exp2 SIRS_19exp2 SIRS_23exp1
1 25 18.0 36
2 25 18.0 37
3 25 18.0 38
4 25 19.0 37
5 24 18.5 37