Question: some errors in cytofWorkflow2 description
0
11 months ago by
o.hunewald0 wrote:

Hello,

Following the cytofWorkflow2 tutorial I encountered a few bugs:

1. The url argument in

download.file(paste0(url, "/", fcs_filename), destfile = fcs_filename, mode = "wb")

is not specified.

url <- "http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow"

2. The naming of the downloaded files is not the same as defined in the PBMC_md table from Catalyst package. Therefore the following line is creating the next error:

fcs_raw <- read.flowSet(md$file_name, transformation = FALSE, truncate_max_range = FALSE) 3. The arguments for constructing a daFrame are in a different order then in the CATALYST documentation: # Construct daFrame daFrame(fcs_raw, md, panel) # construct daFrame CATALYST documentation (daF <- daFrame(PBMC_fs, PBMC_panel, PBMC_md)) 4. The number of rows panel$fcs_colname and colnames(fcs_raw) is different and I get the next error when trying to

# Construct daFrame
daFrame(fcs_raw, md, panel)

Kind regards,

Oliver

cytofworkflow • 190 views
modified 11 months ago by James W. MacDonald50k • written 11 months ago by o.hunewald0

Dear Oliver,

The RMD file you found is an unfinished update to the cytofWorkflow and has not been committed to a BioC repo (it's just in a fork right now).

The official public cytofWorkflow is still at:

http://bioconductor.org/packages/release/bioc/vignettes/CATALYST/inst/doc/differential_analysis.html

And, there is a description of what CATALYST offers at:

http://bioconductor.org/packages/release/bioc/vignettes/CATALYST/inst/doc/differential_analysis.html

But, indeed, we plan to have an update connecting the two.

Best, Mark