Fitting the iDEA model stuck at 0%

[gskoufos]

Hi,

I'm trying to use iDEA in my scRNA-Seq mouse datasets using your tutorial but I'm facing an issue.

I got my (cluster-specific) DE (and non-DE) genes using MAST on a Seurat object and calculated summary statistics. This is how the dataframe holding summary statistics looks like this:

	beta	beta_var
Dynlt1c	-0.004788767	1.532690e-04
Dynlt1f	-0.018210094	8.189469e-04
Dynlt3	0.099825669	1.633012e-03
Dyrk1a	-0.153623041	5.770188e-03
Dyrk1b	-0.047206616	7.495446e-04
Dyrk2	-0.009460417	3.289918e-05
Dyrk3	0.014333879	3.397681e-05
Dysf	0.032546407	1.065623e-03
Dzank1	-0.027355513	3.783456e-04
Dzip1	0.020114404	2.959934e-04
Dzip1l	0.002514212	7.914841e-07

I'm also using the mouseGeneSets you provide through the function data(mouseGeneSets). Here is the output of the command mouseGeneSets[1:3,1:3]:

	GO:0000002	GO:0000003	GO:0000009
Cfl1	0	0	0
Dcaf8l	0	0	0
Syt4	0	0	0

As you can see, I'm using gene names (instead of IDs) in both the mouseGeneSets and MAST results.

Subsequently, I'm creating an iDEA object using the following command:

idea <- CreateiDEAObject(summary, mouseGeneSets, max_var_beta = 100, min_precent_annot = 0.0025, num_core = 10)

After a few seconds, the iDEA object is ready.

The format of the idea@summary table looks like this:

	beta	beta_var
Fam220a	0.003484590	0.0000513549
Fam221a	-0.010439597	0.0002479317
Fam221b	0.008453979	0.0008646627
Fam222a	0.011624834	0.0005858999
Fam222b	0.014648323	0.0002980931
Fam227a	0.032733509	0.0006496645

Finally, I'm executing the following command:

idea <- iDEA.fit(idea, fit_noGS = FALSE, init_beta = NULL, init_tau = c(-2, 0.5), min_degene = 5, em_iter = 15, mcmc_iter = 1000, fit.tol = 1e-5, modelVariant = FALSE, verbose = TRUE)

and the message I get in the console is the following:

## ===== iDEA INPUT SUMMARY ==== ##
## number of annotations: 3794
## number of genes: 16307
## number of cores: 10
## fitting the model with gene sets information...
|                                                                                                                   | 0%, ETA NA

Then, I waited for a long time (more than an hour) but nothing happened. The progress is stuck at 0%.

Any idea what's causing this?

Thank you for your time!

[YingMa0107]

Hi @gskoufos,

Thank you very much for your interest in our package and thank you for providing such a detailed description on the procedures! Based on your description and the output from iDEA, everything looks good to me. So can you provide me the following information or try these:

1)What is your operating system? If your system is Windows, that might be related to the issue that windows does not support mclapply (at least at the time when we implemented the package), a function related to the parallel computing. For this issue, I need to take time to find a replacement for this function.

2)Then perhaps, try to subset 5 gene sets, for example, when you create iDEA object, you can write:

idea <- CreateiDEAObject(summary, mouseGeneSets[,1:5], max_var_beta = 100, min_precent_annot = 0.0025, num_core = 10)

Pleas note that when you subset 5 gene sets, make sure that these gene sets are not filtered (you can check the iDEA input summary ## number of annotations should be > 0). If they are filtered out, just use another 5 or 10 gene sets
This just helps me to see whether it still stuck at 0%.

3. Also, just in case, how many genes are DE genes based on your original MAST output, i.e. p.adjust < 0.05?