Seurat error

Question

[sandy]

Good evening,

I am trying to analysis my scrna-seq data with seurat. Since I combined my data from several databases, thus I want to normalize them first. Then I wrote a for loop, the code is following:

for (i in 1:length(object.list_new)) { 
object.list_new[[i]] <- NormalizeData(object.list_new[[i]], verbose = FALSE)
object.list_new[[i]] <- FindVariableFeatures(object.list_new[[i]], selection.method = "vst", 
                                           nfeatures = 2000, verbose = FALSE) 
 object.list_new[[i]][["percent.mt"]] <- PercentageFeatureSet(object = object.list_new[[i]],  pattern = "^MT-") 
 Feature_range = quantile(object.list_new[[i]]$nFeature_RNA, probs=c(.025,.975))
 Count_range = quantile(object.list_new[[i]]$nCount_RNA, probs=c(.025,.975))
 percent.mt_range = quantile(object.list_new[[i]]$percent.mt, probs=c(.05, .975))
 object.list_new[[i]] <- subset(object.list_new[[i]], subset = nFeature_RNA > Feature_range[1] & nFeature_RNA < Feature_range[2] & percent.mt < 5 & nCount_RNA > Count_range[1] & nCount_RNA < Count_range[2])
 object.list_new[[i]]<- SCTransform(object = object.list_new[[i]], vars.to.regress = "percent.mt", verbose = FALSE)
  }

But, after running I meet an error, and R said:

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': invalid character indexing.

Could you guys please give me some suggestions on to solve this problem?

Thank you ​

[Mehrdad Zandigohar]

Are you using LoadH5Seurat to load your data?

[sandy]

No, I did not. Since some my data is txt file, and some has 3 files (barcode, matrix, features), thus I use read.table, and read10X to load data.