Errors while running the 'Batch Alignment' workflow

[corwrt]

Hi,

First of all, thanks for this great package. I'm a MSc student doing my project on analysing flow data and I started using your package about a week ago: it has proven to be very valuable to quickly run analyses!

I now want to merge different batches together so I decided to first try your 'batch alignment' workflow to understand the overall procedure.
However, I have come across 2 issues, one that I could solve and the other that I do not really understand.

1st issue

The first one happened when I tried running the prep.cytonorm function, in the 'Batch alignment' step.
I obtained the following error:

Working directory is '.../Spectre-master/workflows/Alignment workflows/Output_Spectre/Output 2 - alignment/1 - ref pre-alignment'
Step 1/3. Mapping data
Step 2/3. Merging data
Step 3/3. Returning data
Step 1/4 - Splitting files for use with original FlowSOM function
Step 2/4 - Running FlowSOM
Error in if (nrow(fsom$data) != nrow(dat)) { : argument is of length zero

After looking at the prep.cytonorm function code, I noticed that in the Step 2/4, the function was doing:

if (nrow(fsom$data) != nrow(dat)) {
        stop("Error - the numer of rows (cells) is different in the starting dataset and the FlowSOM prepared dataset")
    }

For some reason, it seemed like the object fsom$data did not exist.
After checking on rdrr.io for the function description (here), I saw that the code was written as:

if (nrow(fsom$FlowSOM$data) != nrow(dat)){
        stop("Error - the numer of rows (cells) is different in the starting dataset and the FlowSOM prepared dataset")
      }

I decided to re-implement the function in my R script to try and see if it would fix the issue. It indeed fixed the issue. I am not very sure why the code I found on rdrr.io was not the exact same as the one in the package installed on my RStudio environment (I have installed the package last week I think, so I believe I have the most recent version).
Is it an issue you have already come across?

2nd issue

The second issue I have not yet solved is when I am trying to run the train.cytonorm function.
I obtained this error:

Training alignment - setup
Working directory is '/Users/corentinwiscart/Downloads/Spectre-master/workflows/Alignment workflows/Output_Spectre/Output 2 - alignment'
Training alignment - file (batch) preparation
Training alignment - file (batch) and metacluster splitting
Training alignment - learning conversions
Processing cluster 1
Error in (function (files, labels, channels, transformList, nQ = 101,  : 
  Input parameters 'labels' and 'files' should have the same length

I decided to re-iterate what I did for my previous issue and I checked the code of the function. In the learning conversions step, I think my error comes from when the script calls the normMethod.train function (here QuantileNorm.train) with normParams_tmp:

normParams_tmp <- c(normParams,
                            list(files = file.path(getwd(),
                                                   #outputDir,
                                                   paste0(gsub("[:/]", "_", train.files),
                                                          "_fsom", cluster, ".fcs")),
                                 labels = as.character(model$files),
                                 channels = align.cols,
                                 transformList = NULL,
                                 verbose = verbose,
                                 plot = plot))

If I understand correctly, it seems like the argument files is supposed to be the path to .fcs files corresponding to the training dataset? If yes, I did not find any .fcs files in the /data sub-folder of the workflow directory.
I could also have misunderstood it and the .fcs files are supposed to be generated through a previous step but it seems like it is not the case.
Could you provide some guidance on how to solve the issue, if this is something you've already come across or if I am doing something wrong?

I am fairly new to this kind of computational techniques and workflows to analyse flow data so I might have missed a big step, compulsory for the smooth running of the batch alignment workflow, but I tried following the step-by-step tutorial on your website (this one).

Sorry for the long message but I wanted to try and describe the issue in details.
I hope I started the discussion in the right place!

Thanks a lot for your help.

Corentin