I was trying to run deconvolution on my Bulk RNA seq data with multiple samples and I found your to be convenient as I had problems deciding on which method to use. I have my sample matrix as normalized TPMs and I obtained gene signatures of cell types from "celldex" and transformed the provide log counts (normalized as TPM) using :
TPMs_count = exp(log_counts)
and I ran this > decon_rls <- deconvolute(m = TomEMD_dec, sigMatrix = cell_types_means_m, "rls", use_cores= 1)
and obtained this error only running rls
Running deconvolution method "rls" on signature matrix "sig1"
Error in rlm.default(df$x, as.vector(z), maxit = 1000, psi = psi.huber) :
'x' is singular: singular fits are not implemented in 'rlm'
and this error when running dtangle
> decon_dtangle <- deconvolute(m = TomEMD_dec, sigMatrix = cell_types_means_m, "dtangle", use_cores= 1)
Running deconvolution method "dtangle" on signature matrix "sig1"
Warning message:
In max(rowSums(x), na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
and when running svr it run nonstop without finishing
other methods like 'ols','nnls','qprog' run without any problem
xanibas
commented
1 year ago
Dear Authors ,
Thank you for reading my message.
I was trying to run deconvolution on my Bulk RNA seq data with multiple samples and I found your to be convenient as I had problems deciding on which method to use. I have my sample matrix as normalized TPMs and I obtained gene signatures of cell types from "celldex" and transformed the provide log counts (normalized as TPM) using :
TPMs_count = exp(log_counts)and I ran this> decon_rls <- deconvolute(m = TomEMD_dec, sigMatrix = cell_types_means_m, "rls", use_cores= 1)and obtained this error only running rlsand this error when running dtangle
and when running
svrit run nonstop without finishingother methods like
'ols','nnls','qprog'run without any problemCould you help me ?
Thanks, Best