ExperimentHub with zero records

[Pedramto89]

Hi I am trying to use SingleR for annotating my clusters. I would use "Pancreas" datasets but I get this error:

"> query(eh, "BaronPancreasData('human')") ExperimentHub with 0 records snapshotDate(): 2022-10-31"

I tried to use other datasets for pancreas but still get the same error. Would you help me?

[LTLA]

BaronPancreasData('human') is the function call, not the query to ExperimentHub. Just run it as a command.

[Pedramto89]

Thank you! So you mean like this: "BaronPancreasData('human')"? Then, when I want to make the query out of this dataset, how should I do it? This is the workflow I follow: eh <- ExperimentHub() query(eh, "BaronPancreasData('human')")

[LTLA]

Yes, just run it directly. See ?BaronPancreasData for more details.

[Pedramto89]

Thank you it worked. I thought it only has pancreas samples while it has everything other than pancreas. Here is the pipeline I followed:

eh <- ExperimentHub() d <- BaronPancreasData('human') query(eh, "d")

Then, we I run query() like above, it shows that: retrieve records with, e.g., 'object[["EH1"]]'

I do this and run: pdac_ref <- eh[["EH1"]]

In the pdac_ref object I created there is: assayData: 23368 features, 7706 samples

So, as I explained, I am looking for pancreas (tumor samples) which should be in the short from of "PAAD" or "PDAC" while in the metadata there is not:

levels(pdac_ref$CancerType) [1] "BLCA" "BRCA" "COAD" "GBM" "HNSC" "KICH" "KIRC" "KIRP" "LAML" "LGG" "LIHC" "LUAD" [13] "LUSC" "OV" "PRAD" "READ" "SKCM" "STAD" "THCA" "UCEC"

How can I extract the data only for pancreas? Thanks!!

[LTLA]

I don't really know where to start here, because your comments suggest that you have a major misunderstanding of how programming works. query(eh, "d") doesn't make any sense. eh[["EH1"]] has no relevance to the scRNAseq package. Just run BaronPancreasData() and look at the output.

[Pedramto89]

Thank you for questioning my programming skills!!