Data_imputation, the condition has length > 1报错

[sysyangb]

作者你好, 非常感谢你的工具, 我在使用的时候遇到如下报错

starting worker pid=71069 on localhost:11764 at 18:36:48.679
starting worker pid=71163 on localhost:11764 at 18:36:50.100
starting worker pid=71259 on localhost:11764 at 18:36:51.529
[1] "Genes were splited with 2 parts now it is calculating 1"
Error in if (!(grepl("matrix", class(x), ignore.case = TRUE))) { : 
  the condition has length > 1

不过我在我的Pc端运行相同的测试代码,能正常运行

[1] "Genes were splited with 2 parts now it is calculating 1"
Warning in if (!(grepl("matrix", class(x), ignore.case = TRUE))) { :
  条件的长度大于一，因此只能用其第一元素
27242 genes, 2825 cells
Running SAVER with 3 worker(s)
Calculating predictions for 13621 genes using 6713 genes and 2825 cells...

两个版本都是1.0. 请问这个报错如何解决呢?

[BinDuan]

看起来是运行SAVER的时候出了问题，建议试试运行之前加一行代码options(warn=-1),忽略警告信息试试

[sysyangb]

Reference in new

library(Seurat)

options(warn=-1)

expression_profile<-read.table("./crop_stimulated/expression_profile.txt",head=T,row.names=1,sep="\t")
perturb_information_df<-read.table("./crop_stimulated/perturb_information.txt",head=T,row.names=1,sep="\t")
perturb_information<-as.character(perturb_information_df[,1])
names(perturb_information)<-row.names(perturb_information_df)
# If you don't consider off-target effect, this file is not needed.
#sgRNA_information_df<-read.table("./crop_stimulated/sgRNA_information.txt",head=T,row.names=1,sep="\t")
#sgRNA_information<-as.character(sgRNA_information_df[,1])
#names(sgRNA_information)<-row.names(sgRNA_information_df)

# Have a look at expression_profile
dim(expression_profile)   

# For "data_format_example/crop_unstimulated.RData", this function integrates the input data and filters mitochondrial ribosomal protein(^MRP) and ribosomal protein(^RP).
crop_seq_list<-Input_preprocess(expression_profile,perturb_information)

# For data format like "perturb_GSM2396857" generated by 10X genomics, function "Input_preprocess_10X()" will be suitable. Users can also change this data format to the standard format like "data_format_example/crop_unstimulated.RData", then use function "Input_preprocess()" to process it.

#crop_seq_list<-Input_preprocess_10X("./perturb_GSM2396857")
# cell quality control
crop_seq_qc<-Cell_qc(crop_seq_list$expression_profile,crop_seq_list$perturb_information,species="Hs",plot=T)

# data imputation, it may take a little long time without parallel computation.
crop_seq_imputation<-Data_imputation(crop_seq_qc$expression_profile,crop_seq_qc$perturb_information,cpu_num=1)

谢谢您的回复, 但是Data_imputation()函数执行还是报如下错误, 是linux服务器使用网页Rstudio时出现的,我需要重装一下包吗?
[1] "Genes were splited with 2 parts now it is calculating 1"
Error in if (!(grepl("matrix", class(x), ignore.case = TRUE))) { :
the condition has length > 1

[BinDuan]

我自己跑了下，没有发现问题，你检查下你安装的SAVER版本，然后用crop_unstimulated.RData里的数据试试呢？

[sysyangb]

我自己跑了下，没有发现问题，你检查下你安装的SAVER版本，然后用crop_unstimulated.RData里的数据试试呢？

你好,确实是SAVER的原因, 我更新到最新的1.1.3解决了这个问题, 如果使用install.package()只能装到1.1.2. 谢谢了