Loading Flow Files
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@nicolettesipperly-16835
Last seen 1 day ago
United States

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

flowcore list.files • 416 views
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As the error message said, your matrixStats package is corrupt and needs to be reinstalled.

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Ok I see, thank you!

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