I have log-scaled RNA-seq expression data from 13315 genes from 3 samples and a vector of cell-type markers, with 2553 genes corresponding to 8 cell types.
I followed the CellMix tutorial and created an ExpressionMix object from my 13325 x 3 expression matrix (expression.mat) using the ExpressionMix function and setting the gene and sample names using the featureNames and sampleNames functions. I then used the MarkerList function to create a MarkerList object from my named cell-type character vector.
I deconvolved the data using DSA method, where the progress message I got is:
Using ged algorithm: "DSA"
Estimating basis and mixture coefficients matrices from marker features [DSA]
Using 1140/2553 markers to estimate cell proportions:
astrocyte endothel microglia
237 142 75
myelinating.oligodendrocyte neuron newly.formed.oligodendrocyte
181 130 171
Checking data scale ... NOTE [log]
Converting data to linear scale ... OK [base: 2]
Computing proportions using DSA method ... OK
Estimating basis matrix from mixture coefficients [qprog]
Not using any marker constraints
user system elapsed
9.455 0.000 9.342
GED final wrap up ... OK
Then trying to plot the results using profplot(my ExpressionMix object, DSA fit object) throws this error:
Error in `rownames<-`(`*tmp*`, value = c("basis_1", "basis_0")) :
length of 'dimnames'  not equal to array extent
So my questions are:
1. Why am I getting this error
2. Is it possible to get a matrix/data.frame with the results per each sample or all samples other than the profplot? I guess that would probably be the contents of the legends in the profplot, but what do they actually mean?