bennyyclo/cytofin

Cytofin-an R package for CyTOF data integration

cytofin's Issues

Error: not a valid file

Hi,

When calling cytofin_prep_anchors I get the error message as follows:

Error in FUN(X[[i]], ...) :
'/01_analysis/data/data/data_edit/export_Sample_001_concat_normalized_10101B_live.fcs/' is not a valid file

I have attached a picture of the corresponding metadata.

It's not clear why this is not a valid file. Is there any guidance at all?

Thanks,
Vicky

Nested integration

Hi all,

Love the package, seen some great results on my data. Really appreciated all your hard work.

In my dataset I have a series of batches composed of samples derived from severals runs on different days. I have been integrating over just batch, but wonder if it would also be possible to integrate over the runs within at batch. Any ideas?

Thanks,
Kane

unable to get files from FlowRepository

Hi! Is there another way I can get the Sample and Validation dataset files? FlowRepository will not allow them to be downloaded...Thanks!

Error in new_expr[, ref_metals] : subscript out of bounds

Hi!

I'm trying to run Cytofin, and I encountered an issue in the function cytofin_homogenize. I get the error : Error in new_expr[, ref_metals] : subscript out of bounds. After looking into the panel file, I realized it is due to the metal names Dy192Di, Er167Di, and Lu175Di. If I remove them, then the function runs perfectly. What could I do to resolve this issue?

Thank you so much!

Integration for imaging mass cytometry datasets

Hi,

Nice work on the development of Cytofin for integration of mass cytometry datasets. Since I’m working on imaging mass cytometry data, and am looking to integrate publically available datasets, may I ask whether Cytofin can also be used here? Concerning whether the spatial information of cells in each dataset is retained. Thank you!