Dear all,

please would you advise on the following : I am running the package Seurat on the dataset that was published in :

https://www.ncbi.nlm.nih.gov/pubmed/27565351.

https://github.com/broadinstitute/BipolarCell2016

In the article, there are 6 datasets on BIPOLAR cells that are all together in a matrix, and the columns are labelled :

Bipolar1_barcode1, ...., Bipolar1_barcodeXYZ,

Bipolar2_barcode1, ...., Bipolar2_barcodeXYZ,

Bipolar3_barcode1, ...., Bipolar3_barcodeXYZ,

Bipolar4_barcode1, ...., Bipolar4_barcodeXYZ,

Bipolar5_barcode1, ...., Bipolar5_barcodeXYZ,

Bipolar6_barcode1, ...., Bipolar6_barcodeXYZ,

Shall I understand that, when we would like to include multiple experiments in the same matrix, for the analysis with Seurat, we just need to label the columns according to a scheme : ExperimentA_Barcode, ...., ExperimentX_Barcode ;

thanks a lot,

-- bogdan

For better or for worse, Seurat isn't a Bioconductor package, so this board is technically not the right/best place to get help on using it.

That having been said:

1. You are likely seeing the <ExperimentN>_<barcodeY> column names because the same barcodes are used across samples/experiments (where barcode is the cell barcode from a 10x-like experiment, or perhaps the ID of a well in some other type of expt). So, if you have count matrices from different experiments, they may just have the <barcodeY> column names, in which case you will have to prefix it with something unique to the experiment.

2. Just spanking count matrices together from different experiments can be problematic due to batch effects.

   • The upcoming Seruat v3 release has an improved method and documentation on how you might correct for these batch effects, which you can read about here
   • If you want to stay in the Bioconductor universe, take a look at Aaron Lun's simpleSingleCell workflows. In particular, there is a vignette that described how to deal with these batch effects using a mutual nearest neighbors approach.
   • The Macosko lab has a preprint that uses yet another method called LIGER