Hello,
Unfortunately there is not enough information about this processed data:
How have been this data processed?
Whether counts are normalized? If yes, using which method?
However details could be found through the paper, but I am still not sure about the status of this published dataset here.
Best,
Tima
Created by Fatemeh Zebardast Timaa.z Hi Xiaoying, I suspect that you are correct that this file contains normalized counts based on the number of cells indicated in the paper, but you would need to contact the authors of the paper to confirm. I'm sorry we don't have clearer information in the portal. Hi,
I am having the same question relating to the count file normalization in syn21261143: I have checked the link you posted in your answer, however, for filtered_count_matrix.mtx, it is written that the counts are after QC filtering. Wtihin this matrix, it contains 70634 cells . In your published paper, you have 75060 nuclei after QC control, and 70634 cells rest after normalization and preclustering using SCANPY package.
SO, I assume that the filtered_count_matrix.mtx contains counts that have been normalized. Is it correct? Or do I misunderstanding anything in the process?
Thanks in advance.
Best,
Xiaoying Hi Tima,
Information on data generation and processing for the RNAseq data can be found in the folder wiki here: https://www.synapse.org/#!Synapse:syn21261143. I think that should answer your questions!
Best,
Abby
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