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NathanSkene / EWCE

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
https://nathanskene.github.io/EWCE/index.html
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Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead #34

Closed liuhankui closed 3 years ago

liuhankui commented 3 years ago

This last version seems to use ExperimentHub for doing something when I perform bootstrap_enrichment_test. However, in some cases, we do not connect to the internet or cannot access the web service of bioconductor.org. Even I set ExperimentHub(localHub=T), I still not have a local cache. So, I can not use this package anymore.

liuhankui commented 3 years ago

I guess the issue comes from check_ewce_genelist_inputs

NathanSkene commented 3 years ago

Hey Alan, any thoughts on this one?

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I guess the issue comes from check_ewce_genelist_inputs

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Al-Murphy commented 3 years ago

Hi @liuhankui,

A requirement of Bioconductor is that no large (>5kb) data files can be included in the package submission. The workaround is to submit reference datasets to ExperimentHub. bootstrap_enrichment_test uses reference datasets to run, for example, to check if the inputted human gene lists have mouse homologs by calling check_ewce_genelist_inputs (as you pointed out). The relevant dataset is: 

eh <- ExperimentHub::ExperimentHub()
eh[["EH5367"]])

Can I ask why you need to run EWCE offline? The reference datasets were not set up to allow local calls to ExperimentHub, see neurogenomics/ewceData/utils.R and the get_ExperimentHub function. To rewrite EWCE and ewceData to allow localHub runs would take a significant amount of work given the necessary propagation of a parameter through all instigated EWCE functions so I would like to understand the need.

Thanks, Alan.

liuhankui commented 3 years ago

Hi @liuhankui,

A requirement of Bioconductor is that no large (>5kb) data files can be included in the package submission. The workaround is to submit reference datasets to ExperimentHub. bootstrap_enrichment_test uses reference datasets to run, for example, to check if the inputted human gene lists have mouse homologs by calling check_ewce_genelist_inputs (as you pointed out). The relevant dataset is:

eh <- ExperimentHub::ExperimentHub()
eh[["EH5367"]])

Can I ask why you need to run EWCE offline? The reference datasets were not set up to allow local calls to ExperimentHub, see neurogenomics/ewceData/utils.R and the get_ExperimentHub function. To rewrite EWCE and ewceData to allow localHub runs would take a significant amount of work given the necessary propagation of a parameter through all instigated EWCE functions so I would like to understand the need.

Thanks, Alan.

Hi, Alan, Thank you for explaining why the issue coming out.

The reason I run EWCE offline is that I am calculating the specificity of a large-scale sc-RNA data in local high-performance computing cluster, where has no connection of the Internet. Most of the time, I performed this kind of study on personal computer. But, as we knew, in the future there will be more and more sc-RNA data, which may require a special computing environment. Please take your time to consider the necessity of rewriting EWCE. There are several ways to figure out this issue. I have calculated the specificity matrix and transferred the matrix to personal computer and run bootstrap_enrichment_test on PC. I can also edit the check_ewce_genelist_inputs function and recompile the package and check the gene list myself. But this way may be challenging for someone who is not good at R program.

Best, Hankui.

Al-Murphy commented 3 years ago

I've created this as issue to go in our dev backlog. Thank you Hankui for pointing this out and note, we will make the change for a future release of EWCE. I'll close this issue for now but do get in touch if something else comes up.

Thanks, Alan.