Error in read.preclustered.datasets(pooled_env) : Feature genes mismatch - need to correct dataset binding matching

[zhaoliyang0429]

Hi，
AN error came out when I was running `read.preclustered.datasets, below is my code , I don't konw what was wrong,

DATA.path<-"/media/sf_sharefolder/seurat_human_mm/similarity/"
pooled_env <- initialize.project(datasets = c("E8.5","E9.5","E10.5","E13.5","E14.5",

•                                           "HE5W", "HE6W","HE7W","HE9W","HE10W","HE13W","HE15W",
  

•                                           "HE17W","HE20W","HE22W","HE23W","HE24W","HE25W"),
  

•                              origins = c("mouseEmbyroheart", "mouseEmbyroheart","mouseEmbyroheart",
  

•                                          "mouseEmbyroheart","mouseEmbyroheart","humanEmbyroheart","humanEmbyroheart",
  

•                                          "humanEmbyroheart","humanEmbyroheart","humanEmbyroheart","humanEmbyroheart",
  

•                                          "humanEmbyroheart","humanEmbyroheart","humanEmbyroheart","humanEmbyroheart",
  

•                                          "humanEmbyroheart","humanEmbyroheart","humanEmbyroheart"),
  

•                              experiments = c("mouseEarly", "mouseEarly","mouseEarly","mouseEarly","mouseEarly",
  

•                                              "human","human","human","human","human","human","human",
  

•                                              "human","human","human","human","human","human"),
  

•                              data.path = file.path(DATA.path, "robustsingle"),
  

•                              work.path = file.path(DATA.path, "robustsingle/analysis"))
  

pooled_env <- read.preclustered.datasets(pooled_env)
Computing
Loading /media/sf_sharefolder/seurat_human_mm/similarity//robustsingle/analysis/E8.5/not.regressed

Loading /media/sf_sharefolder/seurat_human_mm/similarity//robustsingle/analysis/E9.5/not.regressed

Loading /media/sf_sharefolder/seurat_human_mm/similarity//robustsingle/analysis/E10.5/not.regressed

Loading /media/sf_sharefolder/seurat_human_mm/similarity//robustsingle/analysis/E13.5/not.regressed

Error in read.preclustered.datasets(pooled_env) :
Feature genes mismatch - need to correct dataset binding matching
In addition: Warning message:
In rownames(merged.counts) != rownames(counts) :
longer object length is not a multiple of shorter object length

Please help me. Thanks very much.
Zhaoliyang

[asmagen]

The error indicates that you have provided matrices with incompatible gene sets. I also see that you’re combining human and mouse — please use the dedicated functions to integrate these since they can’t be read in the initialization step together. Feel free to do a pull request if you have code edits to suggest. On Feb 4, 2021, at 9:20 AM, zhaoliyang0429 <[email protected]> wrote: USE CAUTION: External Message. Hi， AN error came out when I was running `read.preclustered.datasets, below is my code , I don't konw what was wrong, DATA.path<-"/media/sf_sharefolder/seurat_human_mm/similarity/" pooled_env <- initialize.project(datasets = c("E8.5","E9.5","E10.5","E13.5","E14.5", "HE5W", "HE6W","HE7W","HE9W","HE10W","HE13W","HE15W", "HE17W","HE20W","HE22W","HE23W","HE24W","HE25W"), origins = c("mouseEmbyroheart", "mouseEmbyroheart","mouseEmbyroheart", "mouseEmbyroheart","mouseEmbyroheart","humanEmbyroheart","humanEmbyroheart", "humanEmbyroheart","humanEmbyroheart","humanEmbyroheart","humanEmbyroheart", "humanEmbyroheart","humanEmbyroheart","humanEmbyroheart","humanEmbyroheart", "humanEmbyroheart","humanEmbyroheart","humanEmbyroheart"), experiments = c("mouseEarly", "mouseEarly","mouseEarly","mouseEarly","mouseEarly", "human","human","human","human","human","human","human", "human","human","human","human","human","human"), data.path = file.path(DATA.path, "robustsingle"), work.path = file.path(DATA.path, "robustsingle/analysis")) pooled_env <- read.preclustered.datasets(pooled_env) Computing Loading /media/sf_sharefolder/seurat_human_mm/similarity//robustsingle/analysis/E8.5/not.regressed Loading /media/sf_sharefolder/seurat_human_mm/similarity//robustsingle/analysis/E9.5/not.regressed Loading /media/sf_sharefolder/seurat_human_mm/similarity//robustsingle/analysis/E10.5/not.regressed Loading /media/sf_sharefolder/seurat_human_mm/similarity//robustsingle/analysis/E13.5/not.regressed Error in read.preclustered.datasets(pooled_env) : Feature genes mismatch - need to correct dataset binding matching In addition: Warning message: In rownames(merged.counts) != rownames(counts) : longer object length is not a multiple of shorter object length Please help me. Thanks very much. Zhaoliyang — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[zhaoliyang0429]

Thank you very much.