No such file as table_dge_cluster 1.txt in the cluster-analysis folder

[EAC-T]

Dear SCA-IRCM,

I'm using the SEURAT example, I have a Seurat Object that I clustered into 10 clusters (0,1,2,3,4,5,6,7,8,9) When I run the signal = cell_signaling(data=data,genes=all.genes,cluster=cluster) I get this: No such file as table_dge_cluster 1.txt in the cluster-analysis folder No such file as table_dge_cluster 2.txt in the cluster-analysis folder No such file as table_dge_cluster 3.txt in the cluster-analysis folder No such file as table_dge_cluster 4.txt in the cluster-analysis folder No such file as table_dge_cluster 5.txt in the cluster-analysis folder No such file as table_dge_cluster 6.txt in the cluster-analysis folder No such file as table_dge_cluster 7.txt in the cluster-analysis folder No such file as table_dge_cluster 8.txt in the cluster-analysis folder No such file as table_dge_cluster 9.txt in the cluster-analysis folder No such file as table_dge_cluster 10.txt in the cluster-analysis folder

Then the checking for signaling between cell types and then I get nothing significant. I'm not sure what it means, I followed the steps in the DEMO.

Any idea what to do ? Note, that I have 2 datasets that I merged together in SEURAT then I clustered them. Thank you for creating this package!

[SCA-IRCM]

Hi EAC-T, This message is normal if you don't use the cluster_analysis() function prior to the cell_signaling() function. This does not affect the result of the cell_signaling() function. The differentially expressed genes are only used to annotate the interactions as specific or not.

If you get nothing significant but you know that you should have interactions you can try one of the following:

• lower a bit the s.score parameter (down to 0.3 should keep the false positive rate at a "correct" level see the paper for more details).
• change the int.type parameter to "autocrine", this should give you a lot of interactions if your cell types are close. Check the "autocrine-paracrine" interactions.
• try to use the tol parameter (see UsersGuide: https://github.com/SCA-IRCM/SingleCellSignalR_v1/blob/master/UsersGuide.html for more details).

Hope this helps.

Thanks for using SingleCellSignalR!

SCA

[mcap91]

Hello,

This is a great response. As a follow up, where is the "specific" annotation label found? Is it in the cell_signaling() result?

Thank you

[mcap91]

Apologies. I was running mouse converted symbols with mouse gene names in the dge_table. Once they were matched, the "specific" annotation is indeed in the cell signaling() result in the interaction type column.