newSCESet and SingleCellExperiment basic differences and TMM Normalization

Question

[hkarakurt]

Hello everyone,

I am trying to replicate a single cell RNA-Seq data analysis. Actually, the main problem is version. The old results were generated via newSCESet and normalized with normaliseExprs command (TMM method) but for the newest version of R, Bioconductor and packages so I used SingleCellExperiment command.

But I still do not understand what are the differences between the outputs of newSCESet and SingleCellExperiment. I have looked but could not find any information. Mostly pData and fData converted to colData and rowData

They look the same but in the end, but the results look.

I also want to do TMM normalisation but normalizeExprs command is also deprecated. Is there another way to do TMM normalization?

Thank you.

[sgujja]

Hi,

Can you please let me know if you have figured out the TMM normalization with the latest package.

Thanks Sharvari