an error when use check_sce() function
SiyuanHuang1 opened this issue · comments
As you said before (#35), I downloaded the three files manually: modeling_results, sce, sce_layer. But when I tried to convert sce to spe object, error happened. I used check_sce(), there was the same message.
Code
library(spatialLIBD)
load("Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata")
load("Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata")
load("Human_DLPFC_Visium_modeling_results.Rdata")
spe <- sce_to_spe(sce)
check_sce(sce)error information
Error in check_sce(sce) :
Not all of all(c("imagerow", "imagecol", "sample_name", "key", variables) %in% .... are TRUEI found this was because the downloaded sce object didn't include the ManualAnnotation and spatialLIBD columns
#the variables vector is from check_sce() source code
> c("imagerow","imagecol","sample_name","key",variables)[! c("imagerow","imagecol","sample_name","key",variables) %in% colnames(colData(sce))]
[1] "ManualAnnotation" "spatialLIBD"
So the ManualAnnotation and spatialLIBD are important? could you provide them as .Rdata for us?
or should I delete these terms in check_sce() code for smooth running?
R session information
options(width = 120)
sessioninfo::session_info()
- Session info -------------------------------------------------------------------------------------------------------
setting value
version R version 4.1.2 (2021-11-01)
os Windows 10 x64 (build 19042)
system x86_64, mingw32
ui RStudio
language (EN)
collate Chinese (Simplified)_China.936
ctype Chinese (Simplified)_China.936
tz Asia/Taipei
date 2022-03-04
rstudio 1.3.1073 Giant Goldenrod (desktop)
pandoc 2.10 @ D:\\hsy\\software\\anaconda\\Scripts\\pandoc.exe
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[1] D:/hsy/software/R-4.1.2/library
D -- DLL MD5 mismatch, broken installation.
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Hi,
I believe that you meant to use check_spe() not the one that ends in sce.
Best,
Leo
No, maybe my code confused you. I re-show it:
> load("D:/hsy/project/ST/data/DLPFC/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata")
> check_sce(sce)
Error in check_sce(sce) :
Not all of all(c("imagerow", "imagecol", "sample_name", "key", variables) %in% .... are TRUE
> spe <- sce_to_spe(sce)
Error in check_sce(sce) :
Not all of all(c("imagerow", "imagecol", "sample_name", "key", variables) %in% .... are TRUE
The reason is that there is not ManualAnnotation&spatialLIBD in Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata
Hi @SiyuanHuang1 ,
I tried reproducing your error and couldn't initially:
master > sce <- fetch_data("sce")
snapshotDate(): 2022-03-01
2022-03-04 19:00:27 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/3ae9464272d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
master > check_sce(sce)
class: SingleCellExperiment
dim: 33538 47681
metadata(1): image
assays(2): counts logcounts
rownames(33538): ENSG00000243485 ENSG00000237613 ...
ENSG00000277475 ENSG00000268674
rowData names(9): source type ... gene_search is_top_hvg
colnames(47681): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
TTGTTTCCATACAACT-1 TTGTTTGTGTAAATTC-1
colData names(74): barcode sample_name ... spatialLIBD
ManualAnnotation
reducedDimNames(6): PCA TSNE_perplexity50 ...
TSNE_perplexity80 UMAP_neighbors15
mainExpName: NULL
altExpNames(0):However, I was forgetting about https://github.com/LieberInstitute/spatialLIBD/blob/master/R/fetch_data.R#L150 which is defined at https://github.com/LieberInstitute/spatialLIBD/blob/master/R/fetch_data.R#L161-L170. So in your case you would need to do this:
library("spatialLIBD")
load("Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata", verbose = TRUE)
## You could use the same name, but I'm using different ones here for clarity
updated_sce <- spatialLIBD:::.update_sce(sce)
## Note the ::: and not the :: in the line above, that's because .update_sce() is a non-exported function in spatialLIBD
check_sce(updated_sce)
## Continue along ^^Have a good weekend!
Best,
Leo
I got it! Thank u for your advice
Hi，
I followed the steps, but I still encountered an error in the final step. What should I do to resolve it?
library("spatialLIBD")
load("Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata", verbose = TRUE)
You could use the same name, but I'm using different ones here for clarity
updated_sce <- spatialLIBD:::.update_sce(sce)
Note the ::: and not the :: in the line above, that's because .update_sce() is a non-exported function in spatialLIBD
check_sce(updated_sce)
