Entering edit mode
Dear All,
I am using R version 3.3.1 (R version 3.3.2 (2016-10-31)) , and trying to run the single cell workflow from here https://www.bioconductor.org/help/workflows/simpleSingleCell/#detecting-marker-genes-between-subpopulations and when I used the functions from Scran library, its says function not found. For instance, the same happened to setSpike, findMarker functions
Any help would be great
Thank you
biocLite. These updates often contain important bug fixes and improvements - not just for scran, but for other Bioconductor packages - and you are only hurting yourself by sticking to older versions. Sooner or later, you will need to do this, so why not now?findMarkersneeds to be applied on the single-cell expression matrix, not on the limma results. The function will then identify the top set of marker genes that are DE in each group compared to each other group. (Note that theTopfield in the output requires some care during interpretation, so read the documentation). You may also be interested inoverlapExprs, which will give you an idea of how much the expression distributions overlap between two groups - good markers should exhibit very low overlap (values near 0 or 1).