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xuranw / MuSiC

Multi-subject Single Cell Deconvolution
https://github.com/xuranw/MuSiC
GNU General Public License v3.0
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Error: Not enough cell types! when do the cell type proportion estimates #33

Open Jia21 opened 5 years ago

Jia21 commented 5 years ago

Hi,

I have a question on cell type proportion estimates. I have a single cell RNA-seq reference data like the below toy example, Genes CD4 Mono Ery ACE 49 1 0 ALG9 401 74 234 ANKRD18A 332 69 0 AQP1 14 0 8342 CELF6 40 17 0 CFB 206 100 14

When I do music_prop(bulk.eset = bulk.est, sc.eset = scRNA.est, clusters = 'cellType', samples = 'sampleID', select.ct = c('CD4', 'Mono','Ery'), verbose = F). It throws out an error as

Error in music_prop(bulk.eset = bulk.est, sc.eset = scRNA.est, clusters = "cellType", : Not enough valid cell type!

In order to help you understand, I attach the info of scRNA.est below, image

I am wondering that whether MuSiC needs at least two replicates for inferring the cell type proportion.

Thanks a lot! Elaine

xuranw commented 5 years ago

Hi Elaine,

Yes, we need at least two replicates for cell type proportions because we need to calculate cross-subject variance.

Best, Xuran

Jia21 commented 5 years ago

Hi Elaine,

Yes, we need at least two replicates for cell type proportions because we need to calculate cross-subject variance.

Best, Xuran

Hi Xuran,

Thanks for your reply! I am wondering what the meaning of the subjects, samples or cell types? I assume subjects denote samples in bulk RNA, and I thought the replicates are for calculation of cross-cell-types variance.

Thanks a lot !

Elaine