How to compare transcriptomic profiles of two cell types (single cell RNA-seq)? I found this interesting Single RNA-seq data set in GEO, but I am not sure how to analyze it appropriately.

They have deposited transcriptomic profiles of human and mouse pancreatic islets (pancreatic cells: Beta cells, Delta, etc).  The problem I see is that the different pancreatic cell types are not in equal numbers: 872 Beta cells and 214 Delta cells.

I want to see whether the expression of a set of genes are correlated between the two cell types. I don't think that I can visualize the correlation between the expression of the Beta and Delta cells on a scatter plot if they are unequal in number. Is there a workaround to include all the cells in the analysis, without losing good quality transcriptome of beta/delta cell?

What I would like to do is to compare the expression of two pancreatic cell types (Beta v.s. Delta cells) using a scatter plot. I have a set of genes that I am interested in, and would like to see their expression profile for beta and delta cells. As far as I know, it is only possible to visualize this using a scatterplot (X:Beta vs Y:Delta) where the number of isolated beta cells is the same as the number of delta cells.

Question: Given unequal number of isolated panacriatic cells, what would be an appropriate way to compare the expression profiles? Should I just ignore the extra ones? 

Any idea how to approch this problem?

Thanks,
You are looking for a way to compare expression profiles between cell types, and your data is counts of genes expressed per cell. Your issue is that the data is highly dimensional. It has as many dimensions as you have genes. To be able find useful information, you must reduce these dimensions using a statistical technique such as Principal COmponents Analysis (PCA), t-Distributed Stochastic Neighbor Embedding (t-SNE), or Multidimensional Scaling (MDS). The result of these analyses is a reduction of your thousands of dimensions to vectors (eigenvectors in PCA) of variance which you can plot against each other in a scatter plot.

I have been working with Single Cell RNA-seq data and have been exploring the difference in gene expression in a certain type of cells between timepoints. Seurat (R package) is a very powerful tool for scRNA-Seq data analysis. 

Here is a a tSNE of my data. I have added the timepoint labels, but you can see that after performing the dimensionality reduction the two different timepoints cluster by their gene expression profiles. I can then use Seurat to see which specific genes are differentially expressed between the clusters and a whole bunch of other fun things.