Open Jinqingchang opened 2 months ago
Thank you for your feedback. The sample information in the output of SEVtras.ESAI_calculator has been sorted by sample name. You can find the same sEVs based on batch information in adata.obs['batch'].
In addition, the SEVtras score has been filtered by SEVtras.sEV_recognizer in sEVs_SEVtras.h5ad by default. If you want to change the threshold, I recommend to use the parameter score_t
, e.g. score_t='15'
.
Thank you for your feedback. The sample information in the output of SEVtras.ESAI_calculator has been sorted by sample name. You can find the same sEVs based on batch information in adata.obs['batch'].感谢您的反馈意见。 SEVtras.ESAI_calculator 输出中的样本信息已按样本名称排序。您可以根据 adata.obs['batch'] 中的批次信息找到相同的 sEV。 In addition, the SEVtras score has been filtered by SEVtras.sEV_recognizer in sEVs_SEVtras.h5ad by default. If you want to change the threshold, I recommend to use the parameter
score_t
, e.g.score_t='15'
. 另外,SEVtras分数默认已经被sEVs_SEVtras.h5ad中的SEVtras.sEV_recognizer过滤。如果您想更改阈值,我建议使用参数score_t
,例如score_t='15'
。
Thank you for your quick reply, but I still have some concerns. The batch information in obs and the sample information in obsm of the SEVtras_sEVs.h5ad file itself do not correspond, even though both represent the source sample of the barcode.This does not seem to be related to sorting.
For example, the barcode AAACCCAGTGGATACG-1
has inconsistent batch information in obs and sample information in obsm.
Could your please try to find AAACCCAGTGGATACG-1-1
AAACCCAGTGGATACG-1-2
AAACCCAGTGGATACG-1-3
.... in output adata?
In my tests, the information in adata.obs['batch'] and adata.obsm['source']['sample'] would be the same.
This will cause an error because the index of the output file sev_sEVs.h5ad from the ESAI_calculator function is not named as you mentioned. In fact, the barcode I showed in the first comment is the result of my own adjustment, aiming to match the barcodes in the SEVtras_sEVs.h5ad file with those in the SEVtras_combined.h5ad file. Otherwise, the barcodes of these two files would not correspond. This is not the output result of the ESAI_calculator function.
When I do not make any modifications to the output file and directly check the file output by the ESAI_calculator function, the obs of the two files are as shown in the two images above. The obsm of the SEVtras_sEVs.h5ad file is as shown in the image below.
I tried the last barcode
TTTGGTTCACTACCGG-1-1
; it is inconsistent between obs
and obsm
.
You don't need to match the cell barcode names in the two files. Here's why:
First, the cell barcode in SEVtras_combined.h5 is suffixed by '1-1', '1-2', etc. because the same barcode is in different single-cell samples. I suggest that you can add some different character to distinguish them.
Second, SEVtras obtains sample or batch information only in the first step (SEVtras.sEV_recognizer). However, the inputted adata_cell file in the second step still contains the same barcodes with the adata_ev. This causes the barcodes in the adata_combined to have an extra '-1' (from -1 to -1-1, from -1-2 to -1-1-2). Simply change the cell barcode in the adata_ev with a certain character, such as an 'E' (from AAACCCAGTGGATACG-1
to AAACCCAGTGGATACG-1E
), and re-run SEVtras.ESAI_calculator.
By the way, I suspected that the cell barcode in your samples may have been replaced by certain software, which is not the real one.
Thank you for your kind reminder. I will review my data processing steps carefully. If there are no errors in the execution, I will get back to you.
Dear Developer,
Thank you for creating such a useful tool.
I encountered some issues while using the ESAI_calculator function. Initially, I performed sEV_recognizer with multiple samples using the following code:
The resulting sEV files contain batch information.![图片](https://github.com/bioinfo-biols/SEVtras/assets/167421502/b3639c41-ebbb-4982-b7e0-b24872ac4121)
I then used the ESAI_calculator function, and the output in SEVtras_sEVs.h5ad under obsm contains source information with both type and sample fields.
However, the sample information does not correspond to the output from sEV_recognizer.![图片](https://github.com/bioinfo-biols/SEVtras/assets/167421502/a0abd3c2-3f46-45a3-aef8-9b6d25b44b27)
I am unclear about the reason for this discrepancy. Could you please clarify which result is correct?