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phipsonlab / speckle

R package for analysing single cell data
GNU General Public License v3.0
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Error: Subsetting to non-estimable coefficients is not allowed. #8

Closed dn-ra closed 1 year ago

dn-ra commented 1 year ago

Hi,

Thanks for your efforts with this tool.

It's my first time using propeller but I'm getting this error with my data using command propeller(clusters = as.factor(seu_batch1_cluster_1to6$seurat_clusters), sample = as.factor(seu_batch1_cluster_1to6$orig.ident), group = as.factor(seu_batch1_cluster_1to6$group))

Performing logit transformation of proportions
group variable has > 2 levels, ANOVA will be performed

Coefficients not estimable: DNFB_OT-I HSV_gBT HSV_OT-I 
Warning: Partial NA coefficients for 7 probe(s)Coefficients not estimable: DNFB_OT-I HSV_gBT HSV_OT-I 
Warning: Partial NA coefficients for 7 probe(s)Error in `[.MArrayLM`(fit, , coef[-1]) : 
  Subsetting to non-estimable coefficients is not allowed.

Any ideas? I've tried subetting the data so that it has fewer clusters and fewer groups, but no luck. Strangely, it also fails to show vignettes and I have tried to various installation options shown in the git:

> browseVignettes('speckle')
No vignettes found by browseVignettes("speckle")

Many thanks, Dan

Here's a link to the Rds file with the data I'm inputting: https://unimelbcloud-my.sharepoint.com/:u:/g/personal/daniel_rawlinson_unimelb_edu_au/EUxEKhF4lDNFveH_tpzSAdIBAQqQh4pjpPnVwccV5lMnAw?e=wP24kP

dn-ra commented 1 year ago

I solved it.

If you are supplying a vector of samples and a vector of groups to the function, you may need to paste the group and sample together to use as the argument for sample so that the number of levels sample = ngroups(group) x ngroups(sample)