db = 'none' is not working

[Jessie Huang]

Hello, I have some problems when using the new db = 'none' parameter in the "train_cell_classifier" function. My garnett version is:

> packageVersion("garnett")

[1] '0.1.3'

But when I use:

> classifier <- train_cell_classifier(cds = new_cds,

+                                          marker_file = marker_file_path,

+                                          db='none',

+                                          cds_gene_id_type = "SYMBOL",

+                                          num_unknown = 50, #lower the training for unknown

+                                          marker_file_gene_id_type = "SYMBOL")

Error: db must be an 'AnnotationDb' object see http://bioconductor.org/packages/3.8/data/annotation/ for available

The error keeps warning me that db must be an 'AnnotationDb' object...

Did I do something wrong here?

Thanks for your help in advance,

Best.

[Hannah A Pliner]

Hi,

I believe that the db="none" feature was released in version 0.1.4. Go ahead and repeat the installation instructions on the website to get the latest release. Let me know if this doesn't solve the issue.

Best,

Hannah Pliner, Ph.D.

Lead Data Scientist for Single Cell Genomics

Brotman Baty Institute for Precision Medicine

Health Sciences Building (HSB) H564E

Seattle, WA

206-616-0454

hpl...@uw.edu

--
You received this message because you are subscribed to the Google Groups "garnett-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to garnett-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/garnett-users/590fa375-b98a-4edd-b757-934b821d75ba%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Jessie Huang]

Thanks so much for the quick response. I got the training of the classifier working, however, I encounter another error in the "classify_cells" part. When I use:

> query_cds <- classify_cells(query_cds , classifier,

+                                           db = org.Mm.eg.db,

+                                           cluster_extend = TRUE,

+                                           cds_gene_id_type = "SYMBOL",

+                                           verbose = TRUE)

The verbose message give:

``````````````````````

Starting classification

Checking inputs

Normalizing CDS object

Converting CDS IDs to ENSEMBL

No garnett_cluster column provided, generating clusters for classification

Predicting cell types

<simpleError in rowQ(imat, ncol(imat)): cannot handle missing values.>

Complete!

````````````````

It said the classification is complete, but when I check the metadata, it gives all unknown prediction. I checked my cds data type and classifier, there shouldn't be any NA values in them..

I there anything I doing wrong here?

Thanks for your time and help,

Best,

Jess

To unsubscribe from this group and stop receiving emails from it, send an email to garnet...@googlegroups.com.

[Hannah A Pliner]

I believe this issue is solved in the most recent version of the monocle3 branch and I will push a fix to the master branch shortly. Go ahead and give it another try, thanks for you patience!