[BioC] CellMix package use with own data matrix

[Renaud Gaujoux]

Hi Maria,

note that you do not need to use an ExpressionSet object. Plain matrix
objects should work as well, as long as the rownames match:

x <- as.matrix(read.table('mixed_
data.tsv', sep = "\t"))
y <- as.matrix(read.table('celltype_data.tsv', sep = "\t"))
res <- gedProportions(x, y, rescale = FALSE, log = FALSE, normalize = FALSE)

# unscaled proportions
coef(res)
# rescaled proportions (sum up to one)
scoef(res)

If you later want to create an ExpressionSet then it just about
wrapping the matrix object:

eset <- ExpressionSet(x)

but this does not make much sense if you do not have extra phenotypic
data or gene annotation package name to associate your gene expression
data with.

Hope this helps.
Please let me know if this works fine for you.

Bests,
Renaud