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SCDC
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Fine tuning of parameters for particular populations #38

Open Goultard59 opened 1 year ago

Goultard59 commented 1 year ago

Hello,

bulk entry: 192 samples of bulk RNAseq from 4 conditions, six samples with eight replicates each scRNAseq: 12 samples from 2 conditions 3-time points with two replicates providing 11 clusters

Codes run perfectly with these commands

bulkseger.scxin <- SCDC_prop(bulk.eset = eset, sc.eset = eset.sc, ct.varname = "seurat_clusters",
                             sample = "SAMP", ct.sub = c("0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11"))

Unfortunately, I observe that the proportions given to cluster 2 are 0 for every sample. I suspect that those proportions go to clusters 0 sexe_bulk

Here is my Differential expression test between clusters 0 and 2

<!DOCTYPE html>

gene | p_val | avg_log2FC | pct.1 | pct.2 -- | -- | -- | -- | -- A230046K03Rik | 0 | 0.9424354 | 0.302 | 0.080 Atf4 | 0 | 0.9636213 | 0.284 | 0.068 BC051077 | 0 | 1.0934125 | 0.270 | 0.051 Btg1 | 0 | 1.0234096 | 0.387 | 0.126 Btg2 | 0 | 2.0308540 | 0.514 | 0.085 C3ar1 | 0 | 0.9859951 | 0.344 | 0.109 Ccnl1 | 0 | 1.4244196 | 0.329 | 0.047 Cd83 | 0 | 1.3736968 | 0.401 | 0.121 Cebpb | 0 | 1.6196460 | 0.465 | 0.143 Chd4 | 0 | 0.8624976 | 0.495 | 0.209 Coq4 | 0 | 1.1222041 | 0.251 | 0.040 Ddx26b | 0 | 1.0279751 | 0.273 | 0.061 Ddx3x | 0 | 0.8229021 | 0.483 | 0.206 Ddx5 | 0 | 0.9960518 | 0.675 | 0.320 Dusp1 | 0 | 1.8613721 | 0.384 | 0.057 Dusp2 | 0 | 1.7916930 | 0.278 | 0.031 Egr1 | 0 | 2.2168216 | 0.848 | 0.231 Fos | 0 | 1.8854204 | 0.568 | 0.129

And here is my differential between cluster 2 and the other clusters <!DOCTYPE html>

gene | p_val | avg_log2FC | pct.1 | pct.2 -- | -- | -- | -- | -- Btg2 | 0 | -1.7712867 | 0.085 | 0.434 C3ar1 | 0 | -0.8627266 | 0.109 | 0.322 Ccnl1 | 0 | -1.0306977 | 0.047 | 0.253 Cd83 | 0 | -1.3607788 | 0.121 | 0.372 Cebpb | 0 | -1.6607110 | 0.143 | 0.453 Ctsc | 0 | -1.2052791 | 0.155 | 0.435 Dab2 | 0 | -1.8072923 | 0.171 | 0.460 Ddx5 | 0 | -0.7751759 | 0.320 | 0.616 Dusp1 | 0 | -2.1763548 | 0.057 | 0.397 Eef1a1 | 0 | 0.4687902 | 0.987 | 0.983 Eef2 | 0 | 0.8944768 | 0.649 | 0.566 Egr1 | 0 | -1.6636821 | 0.231 | 0.668 Fos | 0 | -1.8573273 | 0.129 | 0.503

You can see that clusters do not have particular markers distinguishing them from others. The main difference with cluster 0 is the absence of expression of particular markers.

I would like to know if parameter changes to detect this population are possible.

Thanks for your response. Adrien Dufour.