I am using flowCore, and have updated to the most recent version. I am trying to have the package load the FCS files using list.files. and use them to make the histograms using batchFlowHist. I have used this program before with the same types of data, but now I am getting the error with both my new and old dataset. I am not sure if it is an issue with the data files and how they are downloading or if there is some issue with the way I am writing the code. Thank you for your help!!
source("https://bioconductor.org/biocLite.R") biocLite("flowCore") library(flowCore) biocLite("flowPloidy") library(flowPloidy) Dfiles1<-list.files("052218", full.names = TRUE)# pulls all files from folder Dfiles1 Dfiles1B<-batchFlowHist(Dfiles1, channel="FL2.A", standards=0.55)
>Dfiles1
[1] "052218/SAMPLE (1).004" "052218/SAMPLE.001" "052218/SAMPLE.002"
[4] "052218/SAMPLE.003" "052218/SAMPLE.005" "052218/SAMPLE.006"
[7] "052218/SAMPLE.007" "052218/SAMPLE.008" "052218/SAMPLE.009"
[10] "052218/SAMPLE.010" "052218/SAMPLE.011" "052218/SAMPLE.012"
[13] "052218/SAMPLE.013" "052218/SAMPLE.014" "052218/SAMPLE.015"
>Dfiles1B<-batchFlowHist(Dfiles1, channel="FL2.A", standards=0.55)
processing 052218/SAMPLE (1).004
Error in read.FCS(file, dataset = 1, alter.names = TRUE) :
lazy-load database '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/matrixStats/R/matrixStats.rdb' is corrupt
In addition: Warning messages:
1: In read.FCS(file, dataset = 1, alter.names = TRUE) :
restarting interrupted promise evaluation
2: In read.FCS(file, dataset = 1, alter.names = TRUE) :
internal error -3 in R_decompress1
As the error message said, your matrixStats package is corrupt and needs to be reinstalled.
Ok I see, thank you!