Getting errors from the tutorial.

[ssun12]

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]

Is there any update?

[asmagen]

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