library(devtools)
library(Seurat)
nbt.data=read.table("~/zdata.matrix.txt",sep="\t",header=TRUE,row.names=1)
nbt.data=log(nbt.data+1)
corner(nbt.data)
zf1_p7_S31_umi zf2_dis_S1238_umi zf1_p5_S91_umi zf2_dis_S322_umi
A2ML 0 0 0 1.27680
AAAS 0 0 0 0.00000
AACS 0 0 0 0.00000
AADACL4 0 0 0 0.00000
AAGAB 0 0 0 3.18909
zf2_dis_S1179_umi
A2ML 0.00000
AAAS 2.67415
AACS 0.00000
AADACL4 0.00000
AAGAB 2.67415
dim(nbt.data)
#[1] 11978 1152
nbt=new("seurat",raw.data=nbt.data)
nbt=setup(nbt,project="NBT",min.cells = 3,names.field = 2,names.delim = "_",min.genes = 1000,is.expr=1,)
nbt
An object of class seurat in project NBT
11001 genes across 1069 samples.
nbt=run_tsne(nbt,dims.use = 1:11,max_iter=2000)
[1] "Error : PC1 not found"
Error in La.svd(V) : infinite or missing values in 'x'