I started using ArrayExpress today to read a processed data from a recent study - https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6153/
I used the example provided in the documentation of
() to retrieve and load the data of my interest.
mexp1422 = getAE("E-MEXP-1422", type = "full") ## Build a an ExpressionSet from the processed data cnames = getcolproc(mexp1422) MEXP1422proc = procset(mexp1422, cnames)
I am very puzzled why
() requires exactly one column name. This totally doesn't make sense. In addition, it is very slow for my dataset (19000 single cells). I would like to improve speed by rewriting the code that reads the processed data. I want to use data.table in a way that I suggest here: https://github.com/vitkl/myArrayExpress/commit/53858134241a326dc73f4f70f7fd2622e1702ee5 (line 78). For that, I need to know why
() requires exactly one column name and whether I can remove this condition.