Hello MSBB Team,
We started looking up the omics datasets available for the MSBB study (https://www.synapse.org/#!Synapse:syn3159438) described in https://www.nature.com/articles/sdata2018185, and might have found some discrepancies between the figures reported in the paper and the data available on Synapse.
Specifically, the RNA-seq dataset (https://www.synapse.org/#!Synapse:syn7391833) has a total of 938 samples corresponding to the following brain regions:
BM-10: 261
BM-22: 240
BM-36: 215
BM-44: 222
Total: 938
Now, in the paper (Supplementary table 1 - Sample meta information table after quality control) there are 1282 samples corresponding to RNA-seq. Of these 1282 samples, 23 are marked as "Exclude", so the total number of viable samples would be 1259.
If the above information is correct, then why the total number of RNA-seq samples available in Synapse is only 938?
Thanks,
Sal
Created by Salvatore Loguercio Sal9K Great, thanks very much Minghui and Kara for the explanation! Thanks Minghui, I've updated the wiki to make this more prominent. Hi Sal,
As indicated in "Sample filter" on the wiki https://www.synapse.org/#!Synapse:syn3157743, there are additional samples removed in the assembled expression matrices.
Kara,
You may want to edit the wiki to highlight "sample filter" with a bigger font size or other appropriate method so people will pay more attention.
Minghui Thanks for raising this question @Sal9K. I will follow up with the data provider and report back, however in the meantime if you look at the [raw data](https://www.synapse.org/#!Synapse:syn7416949), all of the samples are present there.
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