Disconnected from server

[hfberg]

Another problem: I successfully produce a single-cell identification for my data set (fine.tune =T), upload to SingleRbrowseR, the uploading is completed but then I get disconnected from the server. I've tried with both .rds and .Rdata. Have I created the S4 object properly? my raw_DGE is 10000 cells and 18264 genes.

code: (Sorry, I deleted the output, but I found no apparent errors)

#fine tune = TRUE
library(SingleR)
raw_DGE <- read.table(file = "/home/proj/data/DGE/CP1_DGE.txt", header = TRUE, row.names = 1, colClasses =c("character", rep("numeric", 10000)))
singler7 <- CreateSinglerSeuratObject(counts = raw_DGE, project.name = 'CP1',  species = "Mouse", fine.tune = T)

singler.new = convertSingleR2Browser(singler7)
saveRDS(singler7, 'CP1_singler7.rds')

#accidentally cleared my environment so had to load it again
singler8<-readRDS('/home/proj/tools/SingleR/CP1_singler7.rds')
save(singler8, file="CP1_singler7.RData")

[dviraran]

Hi,

For the web tool you need to upload the rds file. Can you post it so I can see what is the problem?

Thanks, Dvir

[hfberg]

you can download from here: https://drive.google.com/open?id=1WCq_fh6bz5fGid8EsAboD3MlnLhft23y

This dataset is generated from the following code. (Wanted to use you most updated version)

raw_DGE <- read.table(file = "/home/proj/data/DGE/CP1_DGE.txt", header = TRUE, row.names = 1, colClasses =c("character", rep("numeric", 10000)))
singler6 <- CreateSinglerSeuratObject(counts = raw_DGE, project.name = 'CP1',  species = "Mouse", fine.tune = F, reduce.file.size = T)
singler.new = convertSingleR2Browser(singler6)
saveRDS(singler6, 'CP1.rds') 

I have the same browser problem with all different .rds files no matter which exact code I used.

[dviraran]

:) you are saving singler6, not singler.new...

[hfberg]

hahah. yea. that's stupid ;) we can close this one too :)