RuiqiaoHe
commented
8 months ago - The batch information is located in adata.obs['batch'].
- Could you please run the command "SEVtras.ESAI_calculator"? This will give you all the output of SEVtras.
- Could you please read the point 7 in Troubleshooting?
Hello, I am a newbie in single cell analysis, currently familiar with R but not too familiar with python, I have a lot of problems in using your software to process my own data, I hope I can get some help, thank you very much! I re-read your article and software instructions carefully and have some questions from the analysis: 1: When you did the first step of sEV recognition for the 15 tissue samples, did you enter all the samples from different tissues together for the statistics, or did you enter the samples from the same tissues together and the samples from different tissues separately? I am currently analyzing the differences between 11 samples with different trait origins, and I found that putting them together only outputs one raw_SEVtras.h5ad and one sEV_SEVtras.h5ad. the software's output doesn't seem to find the batch information when I read it. 2: What information does each of the output files contain? I input 11 samples, and in addition to getting raw_SEVtras.h5ad and sEV_SEVtras.h5ad, I seem to get 11 folders under the tmp_out path, each of which seems to correspond to one of my input samples, but each of which contains only two files, "itera_gene. txt" and "raw_file.h5ad". I'm not sure exactly which files contain which information and now I'm confused . 3: When I try to convert the h5ad file to h5seurat format using the "Convert" function and read the file in R, I find that I can't read the meta-data. my analysis parameter settings are all the same as in your tutorial. This is the error Adding cell-level metadata Error: Missing required datasets 'levels' and 'values'. Sorry for asking too many questions at the same time. But these are questions I didn't get answered from your published articles and tutorials, and maybe there are other people who are experiencing the same problem. Looking forward to your reply, thank you very much!