error when running xcell

[trptyrphe11]

Input is count matrix of RNAseq;
command: res = deconvolute(exprM, "xcell")

Running xcell
Error in xCell::xCellAnalysis(gene_expression_matrix, rnaseq = rnaseq, :
unused arguments (cell.types.use = cell_types_xcell, parallel.sz = config_env$xcell_cores)

[grst]

This sounds like a problem with xcell. If other methods work well, you should file a bug in the xcell repository (dviraran/xcell). Beware that most methods expect normalized counts (shouldn't matter for xcell, though). If you file a bug, make sure to include a [minimal working example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) to reproduce the problem. Cheers, Gregor

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On Wed, Aug 14, 2019, 19:54 trptyrphe11 ***@***.***> wrote: Input is count matrix of RNAseq; command: res = deconvolute(exprM, "xcell") Running xcell Error in xCell::xCellAnalysis(gene_expression_matrix, rnaseq = rnaseq, : unused arguments (cell.types.use = cell_types_xcell, parallel.sz = config_env$xcell_cores) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#18>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABVZRV2GWEIHGDDHJ45ZFMDQEQFC3ANCNFSM4ILVFGUA> .

[trptyrphe11]

Thanks, actually your comment leads to my second question: would it be possible that add expected data type for each method in the document (for example, count vs normalized (or more specifically tpm/fpkm/etc.)? Thanks.

[grst]

That's a good point. I'll update the documentation and keep this open until then.

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On Wed, Aug 14, 2019, 21:42 trptyrphe11 ***@***.***> wrote: Thanks, actually your comment leads to my second question: would it be possible that add expected data type for each method in the document (for example, count vs normalized (or more specifically tpm/fpkm/etc.)? Thanks. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#18>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABVZRV7Z5WXG4BWUZRVSNDLQEQRW3ANCNFSM4ILVFGUA> .

[grst]

Close #18 per #19.