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asmagen / robustSingleCell

Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.
http://dx.doi.org/10.1016/j.celrep.2019.10.131
MIT License
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Getting errors from the tutorial. #37

Open ssun12 opened 3 years ago

ssun12 commented 3 years ago

Hello,

I am doing a tutorial and getting errors below. I haven't change anything, just followed the tutorial. Can I get a reason why I am getting these errors?

differential.expression.statistics = get.robust.markers( pooled_env, cluster_group1 = c('LCMV2_Tfh_CD4', 'LCMV2_Tfh_Tcmp_CD4'), cluster_group2 = c('LCMV2_CD8_1', 'LCMV2_CD8_2'), group1_label = 'CD4 T Cells', group2_label = 'CD8 T Cells') Coefficients not estimable: groupTRUE Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning messages: 1: Partial NA coefficients for 12897 probe(s) 2: Zero sample variances detected, have been offset away from zero 3: In .ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim, : Estimation of var.prior failed - set to default value 4: non-unique values when setting 'row.names':

plot_pair_scatter(pooled_env, gene1 = 'Cd4', gene2 = 'Cd8a', cluster_group1 = c('LCMV2_Tfh_CD4', 'LCMV2_Tfh_Tcmp_CD4'), cluster_group2 = c('LCMV2_CD8_1','LCMV2_CD8_2'), group1_label = 'CD4 T Cells', group2_label = 'CD8 T Cells') Error in seq_len(n) : argument must be coercible to non-negative integer In addition: Warning messages: 1: In min(plot.data[, 2][plot.data[, 2] != 0]) : no non-missing arguments to min; returning Inf 2: In rnorm(sum(plot.data[, 2] == 0), sd = min(plot.data[, 2][plot.data[, : NAs produced 3: Removed 45 rows containing non-finite values (stat_density2d). 4: In min(x, na.rm = na.rm) : no non-missing arguments to min; returning Inf 5: In max(x, na.rm = na.rm) : no non-missing arguments to max; returning -Inf 6: In max(f) : no non-missing arguments to max; returning -Inf

Also, I got a warning message from the PCA function. How should I use global_objects instead?

Warning message: In slurm_apply(get.shuffled.var, data.frame(rep = seq(nShuffleRuns)), : Argument add_objects is deprecated; use global_objects instead.FALSE

ssun12 commented 3 years ago

Is there any update?

asmagen commented 3 years ago

This package is not maintained at the moment -- please contact if you're interested in collaborating and improving this project.