hansenlab / minfi

Devel repository for minfi
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Error in get(referencePkg): object 'FlowSorted.Blood.EPIC' not found #249

Open yr542 opened 11 months ago

yr542 commented 11 months ago

This is the code I have I tried converting it to 450 and it didn't work so I tried not converting and it still did not work. As EPIC seems to be quite standard now I am unsure of why this is not working? The FlowSorted.Blood.EPIC package has been installed and re-installed several times.

Code:

library("FlowSorted.Blood.EPIC")

estimateCellCounts(RGset, 
                   compositeCellType = "Blood",
                   processMethod = "auto", 
                   probeSelect = "auto",
                   cellTypes = c("Bcell", 
                                 "CD4T", 
                                 "CD8T", 
                                 "Eos", 
                                 "Gran", 
                                 "Mono", 
                                 "Neu", 
                                 "NK"
                                ),
                   referencePlatform = "IlluminaHumanMethylationEPIC",
                   returnAll = TRUE,
                   meanPlot = TRUE,
                   verbose = TRUE)

Error:

Warning message in data(list = referencePkg):
"data set 'FlowSorted.Blood.EPIC' not found"
Error in get(referencePkg): object 'FlowSorted.Blood.EPIC' not found
Traceback:

1. estimateCellCounts(RGset, compositeCellType = "Blood", processMethod = "auto", 
 .     probeSelect = "auto", cellTypes = c("Bcell", "CD4T", "CD8T", 
 .         "Eos", "Gran", "Mono", "Neu", "NK"), referencePlatform = "IlluminaHumanMethylationEPIC", 
 .     returnAll = TRUE, meanPlot = TRUE, verbose = TRUE)
2. get(referencePkg)
3. get(referencePkg)

I also tried everything mentioned in this person's StackExchange post. What do I do to navigate around this?