"Please tell me about the error with FindVariableFeatures. ~Error in '.SelectFeatures（）

[keimiyako]

Hi all! I'm very new to Seurat and scRNA-seq data...
I'm getting a weird error that I have no idea how to fix.
I also couldn't find information about this error.

I've put in my data filtered_feature_bc_matrix (barcodes.tsv.gz, matrixmtx.gz, and features.tsv.gz) as a Seurat object beginning with this:

ctrl.data <- Read10X(data.dir =
"~/Desktop/scRNAseq/outs/filtered_feature_bc_matrix")
ctrl <- CreateSeuratObject(counts = ctrl.data, project = “IMMUNE_CTRL”, min.cells = 5)
ctrl$stim <- “CTRL”
ctrl$replicate <- “n=1”
ctrl <- subset(ctrl, subset = nFeature_RNA > 500)
ctrl <- NormalizeData(ctrl, verbose = FALSE)
ctrl <- FindVariableFeatures(ctrl, selection.method = "vst", nfeatures = 2000)

Yet Continue to get this error each time:

Finding variable features for layer counts.Gene Expression
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts.Multiplexing Capture
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Error in .SelectFeatures():
! None of the features provided are present in the feature set
Run rlang::last_trace() to see where the error occurred.
15 件の警告がありました (警告を見るには warnings() を使って下さい)

rlang::last_trace()
<error/rlang_error>
Error in .SelectFeatures():
! None of the features provided are present in the feature set

---

Backtrace:
▆

1. ├─Seurat::FindVariableFeatures(...)
2. └─Seurat:::FindVariableFeatures.Seurat(...)
3. ├─Seurat::FindVariableFeatures(...)
4. └─Seurat:::FindVariableFeatures.StdAssay(...)

5. ├─SeuratObject::VariableFeatures(...)
   

6. └─SeuratObject:::VariableFeatures.Assay5(...)
   

7.   ├─SeuratObject::.SelectFeatures(...)
   

8.   └─SeuratObject:::.SelectFeatures.list(...)
   

Run rlang::last_trace(drop = FALSE) to see 1 hidden frame.

I keep encountering the same error consistently.
I'm having a tough time with this function and trying to understand how to fix this error.
How can I resolve this issue?
I really appreciate your help!

[bioshot-dotcom]

I had the same error as you, for me it worked removing any data not related to gene expression after reading them with Read10X()...

[Ryan-Zhengyuan]

I also encountered the same error, while my seurat object consisted of 6 data layers. In my case, I found two layers contained the same features (the two layers derived from the same dataset), so I removed the duplicated layers. It worked in the end by processing the object with the last 5 layers.

[Emily-K-Payne]

I am new to R and running into the same issue. How were you able to delete the duplicated?

[Ryan-Zhengyuan]

Previously, I had 6 datasets, and I created a Seurat object for each of them. After merging 6 objects, I obtained one object with 6 layers. So, what I did was just remove one of the 6 datasets and re-merge an object with 5 layers. Sorry that I cannot provide you with further suggestions because I'm also new to Seurat.

Good luck

[zqumich]

I had the same error as you. Have you solved the problem.