Closed imerelli closed 1 year ago
Hi @imerelli,
There are some things you could do:
minsize
to something bigger than 0, for example 5. This argument what it does is to remove TFs that have less than minsize
target genes in your input matrix. Activities inferred with less than 5 targets tend to be rather noisy.decoupleR::check_corr
to identify which TFs are highly correlated after filtering by your data. If two TFs have high correlation (>.95), you cannot fit a multivariate linear model due to colinearity in the coefficients. Once you identify which TFs are colinear, pick one and remove the other for each pair.Hope this is helpful!
Hi, thank you for your help. Removing the pvalues and increasing minsize to 5 it worked. But in the following test, I tried to split the column of the general logFC for each protein in case1/ctrl and case2/ctrl, and I got the error below, any suggestion?
head(mat) GNE.CASE1.vs.CTR GNE.CASE2.vs.CTR ACTA1 -1.2720848 -0.62230089 ACTB -1.2162731 -0.14167834 ACTBL2 -1.4490482 -0.63023057 ACTN2 -1.4759825 -0.01010101 ACTN4 -1.6024540 0.10946555 ARHGDIA -0.5806452 0.91156463 res_decouple <- decouple(mat, + dorothea, + .source='source', + .target='target', + minsize = 5) Error in
map2()
: ℹ In index: 3. Caused by error inmap()
: ℹ In index: 1. Caused by error inweight_mat %*% mat
: ! requires numeric/complex matrix/vector arguments Runrlang::last_error()
to see where the error occurred.
Hi @imerelli
Could you check if your mat
is a matrix or a dataframe? It needs to be a matrix. Also, check that every element in your matrix is numeric, maybe you have a string somewhere.
Just in case you could also install the latest version of decoupler from github:
remotes::install_github("saezlab/decoupleR")
Thank you for your suggestions.
Hi, I'm trying decoupleR with dorothea on a proteomic experiment. I'm loading a table with gene/protein names, logFC and pvalues, but I'm facing this problem, maybe it is a stupid thing, but I don't know how to proceed.