glmGamPoi
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Published
20 hours ago •
const-ae
const-ae
Error in pseudobulk step
Hi,
I was having issues with my own dataset, so tried running the one given in the vignette and ran into the same problem.
In the vignette, starting in section 3.2 I ran the code from sce <- muscData::Kang18_8vs8() to de_res <- test_de(fit, contrast = stimstim+cellCD4 T cells:stimstim, pseudobulk_by = paste0(stim, "-", ind))
This last command resulted in the following error: Error in value[3L] : Object 'stim' not found. Allowed variables are:
There are no allowed variables listed after the colon. Is there a way to get it to recognize the colData columns? I am running glmGamPoi version 1.8.0.
Thanks for your help!
Hi darcymi,
sorry for the delayed response. I was traveling last week and didn't check my emails.
First of all, thank you for opening the issue; it's always important to hear when things don't work. I tried to run the example that you were referencing, but I cannot reproduce the error:
library(glmGamPoi)
sce <- muscData::Kang18_8vs8()
#> snapshotDate(): 2021-05-18
#> see ?muscData and browseVignettes('muscData') for documentation
#> loading from cache
set.seed(1)
# Take highly expressed genes and proper cells:
sce_subset <- sce[rowSums(counts(sce)) > 100,
sample(which(sce$multiplets == "singlet" &
! is.na(sce$cell) &
sce$cell %in% c("CD4 T cells", "B cells", "NK cells")),
1000)]
# Convert counts to dense matrix
counts(sce_subset) <- as.matrix(counts(sce_subset))
# Remove empty levels because glm_gp() will complain otherwise
sce_subset$cell <- droplevels(sce_subset$cell)
fit <- glm_gp(sce_subset, design = ~ cell + stim + stim:cell - 1,
reference_level = "NK cells")
de_res <- test_de(fit, contrast = `stimstim` + `cellCD4 T cells:stimstim`,
pseudobulk_by = paste0(stim, "-", ind))
head(de_res)
#> name pval adj_pval f_statistic df1 df2 lfc
#> 1 LINC00115 9.488240e-01 1.00000000 4.158485e-03 1 53.36198 -0.5418114
#> 2 NOC2L 5.827811e-01 1.00000000 3.054703e-01 1 53.36198 -0.7664476
#> 3 PLEKHN1 9.999228e-01 1.00000000 9.461520e-09 1 53.36198 31.3439440
#> 4 HES4 1.333351e-01 0.93055719 2.323538e+00 1 53.36198 -3.8056793
#> 5 ISG15 6.650242e-05 0.04620493 1.873020e+01 1 53.36198 3.3361152
#> 6 TNFRSF18 5.992403e-01 1.00000000 2.794707e-01 1 53.36198 -0.7194761
Created on 2022-11-14 by the reprex package (v2.0.1)
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Could you run the same code (preferably through reprex) and post the output so that we can figure out why the error occurs for you?
Best, Constantin
