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IMB-Computational-Genomics-Lab / ascend

R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)
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A putative error in Adding additional metadata to the EMSet #12

Closed MichaelPeibo closed 6 years ago

MichaelPeibo commented 6 years ago

Hi, I think I found an error in the tutorial image

actually, this will cause all the THY1 cell.info value 'TRUE', and the later code is correct for certain gene info.

_20180125130429
asenabouth commented 6 years ago

Thanks for bringing this up. The THY1 condition actually refers to the expression of the THY1 PROTEIN. As a part of the experiment, the cells were sorted based on the expression of this surface marker shortly before sequencing. THY1-positive cells were subsequently sequenced as a single batch, while the remaining THY1-negative cells were sequenced as another batch. This is why we are using the information in the batch column of cell information. This is not related to the transcript counts in the expression matrix as the cells may not be expressing this transcript at the time of sequencing. Hope that clears up some confusion.

MichaelPeibo commented 6 years ago

Thanks for attention. It makes sense.