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IMB-Computational-Genomics-Lab / ascend

R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)
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Problem in running scranNormalise #20

Closed mkrzak closed 5 years ago

mkrzak commented 5 years ago

Hello, I wanted to perform normalization with scranNormalise function. I created the newEMSet object in the following way: em <- newEMSet(assays = list(counts = counts) )

Now when Im trying to run command: scran_normalised <- scranNormalise(em, quickCluster = FALSE, min.mean = 1e-05)

Im getting error: Please specify the name of the first column in colInfo as 'cell_barcode'.

However in my colnames(colInfo) in have cell_barcode (as I saw in ascend code it is created automatically when you dont specify it in the newEMSet).

Do you know any possible fix to the problem ?

Best, Monika

asenabouth commented 5 years ago

Hi @mkrzak , Yes, it should automatically assign the first column as cell barcode when you create a new EMSet. I've made a small update to ascend that may address this issue - could you please update your version of ascend and see if you encounter this issue again?

Thanks, Anne

mkrzak commented 5 years ago

Dear Anne, I updated ascend to the latest version on github but the problem still occurs. Best, Monika

asenabouth commented 5 years ago

Hi @mkrzak , Sorry for the delay in responses but I've been able to replicate your issue. I will let you know when I've fixed it.

Thanks for your patience! Anne

asenabouth commented 5 years ago

Hi @mkrzak ,

Please update your version of ascend to the latest version and let me know how you go. You will need to create your EMSet again.

Regards, Anne

mkrzak commented 5 years ago

Dear Anne, Thanks a lot , after updating ascend everything works fine. Best, Monika

asenabouth commented 5 years ago

Excellent @mkrzak ! Thank you for flagging the issue.