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Question: Qualifier / getQAStats: Problem to get statisric from a GatingSet
0
gravatar for veronikag
2.6 years ago by
veronikag0
Germany
veronikag0 wrote:

Hi,

I have one more question to the getQAStats command:

First, I used the following command and it worked:

test <- getQAStats(gs[[1]],isMFI=TRUE)

Second, I tried this command  :

test2 <- getQAStats(gs,isMFI=TRUE)

And I´m getting the following Error:

[1] "extracting stats..."

Error in getQAStats(gs, isMFI = TRUE) :

  Not all IDs for the current sample set are found in meta data of this GatingSet!

 

gs is my GatingSet with 6 samples. With the first command I can extract the statistic for each sample without any errors and warnings.

I would really appreciate your help.

Thank you in advance,

Veronika

ADD COMMENTlink modified 8 months ago by Jiang, Mike1.1k • written 2.6 years ago by veronikag0

getQAStats method for 'GatingSet' was written in the context of QA report and thus not intended to be used without QA preprocess steps. However here is the workaround,

res <- lapply(gs, getQAStats, isMFI = TRUE)

Once you get a list of data.table, it is not difficult to combine them through 'rbindlist'

 

ADD REPLYlink written 2.6 years ago by Jiang, Mike1.1k

Hi Mike,

unfortunately, I´m getting the following Error with your command:

Error in as.list.default(X) : 
  no method for coercing this S4 class to a vector

and I´m not sure, what this is telling me?

Again, I would really appreciate your help!

Best,

Veronika

ADD REPLYlink written 2.6 years ago by veronikag0

I don't know why this is happening. Either your 'gs' variable is no longer a valid 'GatingSet' object or 'lapply' somehow gets masked by some other package. Anyway, start up a fresh R session and try the following reproducible example to see if this works:

library(QUALIFIER)
gs <- load_gs(system.file("/extdata/gs_manual/", package = "flowWorkspaceData"))
res <- lapply(gs, getQAStats, isMFI = TRUE)

Alternatively, try to put namespace explicitly before the lapply:

res <- flowWorkspace::lapply(gs, getQAStats, isMFI = TRUE)

 

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Jiang, Mike1.1k

Thank you! Now, it is working. It was probably masked by some other package.

Best,

Veronika

ADD REPLYlink written 2.6 years ago by veronikag0

Hi Mike,

If I try to do the same, I get: 

library(QUALIFIER)
gs <- load_gs(system.file("/extdata/gs_manual/", package = "flowWorkspaceData"))
res <- flowWorkspace::lapply(gs, getQAStats, isMFI = TRUE)
Error in data.table(channel = thisChnl, stain = thisStain, stats = names(statsOfNode),  : 
  column or argument 3 is NULL

Not sure why?

 

ADD REPLYlink written 8 months ago by biomiha10
0
gravatar for Jiang, Mike
8 months ago by
Jiang, Mike1.1k
(Private Address)
Jiang, Mike1.1k wrote:

I pushed the bug fix to github. Try devtools::install_github("RGLab/QUALIFIER", ref = "trunk)

ADD COMMENTlink written 8 months ago by Jiang, Mike1.1k

Yes, that works now. Thanks.

ADD REPLYlink written 8 months ago by biomiha10
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