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mildpiggy / DEP2

An r package for proteomics data Analysis, developed from DEP.
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Tested contrasts: M_vs_C Error in .ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim, : No finite residual standard deviations #19

Closed AlannaGSpiteri closed 3 days ago

AlannaGSpiteri commented 2 weeks ago

Hi there,

Thanks for this awesome package!

I am trying to run the test_diff function in DEP2 and keep getting errors. The data has been pre-processed (filtered, imputed, normalised etc).

Code: design_formula2 <- formula(~0 + condition + Age + Sex) contrasts3 <- DEP2::test_diff(data_norm2, type = "manual", test = c("M_vs_C"), fdr.type = "BH", design_formula=formula(design_formula2))

Error: Tested contrasts: M_vs_C Error in .ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim, : No finite residual standard deviations

I dont get errors if i just add sex or age alone.

This is basically what the matrix looks like: 2x conditions (C and M), Age, Sex (M and F)

model_matrix conditionC conditionM Age SexM C_4 1 0 60 0 M_10 0 1 62 0 M_7 0 1 80 0 M_4 0 1 76 0 M_2 0 1 63 0 M_3 0 1 70 0 C_1 1 0 64 1 M_5 0 1 65 1 C_3 1 0 52 1 C_5 1 0 76 1 M_9 0 1 77 1 M_1 0 1 54 1 M_8 0 1 79 1 M_6 0 1 78 1 C_2 1 0 78 1

Thanks heaps