Sample label in comb_obj doesn't match

[SamWell16]

I tried to figure out what might cause this issue, but everything seems ok in my single object files and combo file. Could you please help me to fix this issue? What does "sample label" refers to in this error?

Error in cluster_map(marker_file_list, edge_cutoff = 0.1, output = "pbmc", :
Sample label in comb_obj doesn't match names(new_group_list) or names(single_obj_list).

Many Thanks

[peixiaoya]

I also have this problem. I'm confused, too.

[xgaoo]

The sample label means the names of the data objects. "p7d" and "p7e" are the sample labels in the following example.

library(ClusterMap)
marker_file_list <- c(p7d = 'pre_analysis/p7d.markers.csv', p7e = 'pre_analysis/p7e.markers.csv')
res <- cluster_map(marker_file_list, edge_cutoff = 0.1, output = 'p7')
res

ClusterMap requires the sample labels to be the same for the lists of marker_file_list, single_obj_list and comb_obj.

Please send me the command lines you ran if there is still some problems.

[drfinder21]

Sample label in comb_obj doesn't match names(new_group_list) or names(single_obj_list)

[drfinder21]

CTL
An object of class Seurat
19518 features across 4464 samples within 1 assay
Active assay: RNA (19518 features, 2000 variable features)
3 dimensional reductions calculated: pca, umap, tsne

$OV
An object of class Seurat
19808 features across 4375 samples within 1 assay
Active assay: RNA (19808 features, 2000 variable features)
3 dimensional reductions calculated: pca, umap, tsne

res <- cluster_map(marker_file_list, edge_cutoff = 0.2, output = 'SOOV', single_obj_list = single_obj_list, comb_obj = objList$SOOV)
match sub-clusters
circos plot
recolor CTL
[1] "Using Seurat v3"
[1] "Using Seurat v3"
Saving 7 x 7 in image
Saving 7 x 7 in image
recolor OV
[1] "Using Seurat v3"
[1] "Using Seurat v3"
Saving 7 x 7 in image
Saving 7 x 7 in image
Error in cluster_map(marker_file_list, edge_cutoff = 0.2, output = "SOOV", :
Sample label in comb_obj doesn't match names(new_group_list) or names(single_obj_list).
In addition: Warning message:
In levels(sample_label) == names(new_group_list) :
longer object length is not a multiple of shorter object length

[drfinder21]

Coulc you, please, help? I get a cercle claster and a heatmap, but cannot generate a a t-SNE.
Thank you

[drfinder21]

a simple run works
es
CTL OV similarity regroup
1 CTL__10 OV__9 0.60 1
2 CTL__9 OV__8 0.57 2
3 CTL__1;CTL__3 OV__0 0.55 3
4 CTL__0 OV__5 0.51 4
5 CTL__8 OV__6 0.46 5
6 CTL__2;CTL__4;CTL__7 OV__4 0.42 6
7 CTL__11 OV__7 0.34 7
8 CTL__5 OV__2 0.26 8
9 CTL__12 NA 9
10 CTL__13 NA 10
11 CTL__6 NA 11
12 OV__1 NA 12
13 OV__3 NA 13

[drfinder21]

does it work with UMAP.RDS ?

[drfinder21]

marker_file_list <- c(CTL = 'CTL.markers.csv', OV = 'OV.markers.csv')

fList <- c(CTL = 'CTL.RDS', OV = 'OV.RDS', SOOV = 'SOOV.RDS')
objList <- lapply(fList, readRDS)

single_obj_list <- c(CTL = objList$CTL, OV = objList$OV)
head(single_obj_list)

res <- cluster_map(marker_file_list, edge_cutoff = 0.2, output = 'SOOV', single_obj_list = single_obj_list, comb_obj = objList$SOOV)

[xgaoo]

I updated the code to print out more messages. Please try again. Please show me ***@***.***) if it still doesn't work. I guess the sample names in SOOV may be not with prefix of OV or CTL. &nbsp; &nbsp; ------------------&nbsp;Original&nbsp;------------------ From: ***@***.***&gt;; Date: &nbsp;Sat, Oct 2, 2021 01:07 AM To: ***@***.***&gt;; Cc: ***@***.***&gt;; ***@***.***&gt;; Subject: &nbsp;Re: [xgaoo/ClusterMap] Sample label in comb_obj doesn't match (#17) &nbsp; marker_file_list <- c(CTL = 'CTL.markers.csv', OV = 'OV.markers.csv') fList <- c(CTL = 'CTL.RDS', OV = 'OV.RDS', SOOV = 'SOOV.RDS') objList <- lapply(fList, readRDS) single_obj_list <- c(CTL = objList$CTL, OV = objList$OV) head(single_obj_list) res <- cluster_map(marker_file_list, edge_cutoff = 0.2, output = 'SOOV', single_obj_list = single_obj_list, comb_obj = objList$SOOV) — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[drfinder21]

Thank you. how can I e-mail you direcly?

[drfinder21]

should be visible, my @.***