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Nanostring-Biostats / NanoStringNCTools

Tools for NanoString Technologies nCounter Technology for reading RCC files into an ExpressionSet derived object, QC and normalization.
MIT License
9 stars 6 forks source link

Tutorial link #12

Closed amarinderthind closed 3 years ago

amarinderthind commented 3 years ago

Could you please provide the tutorial link on the Github page? or relevant documents

NicoleEO commented 3 years ago

@amarinderthind, we are working on getting the readme up. If you need some guidance in the meantime here is a link to the vignette: https://github.com/Nanostring-Biostats/NanoStringNCTools/tree/master/vignettes.

amarinderthind commented 3 years ago

Thanks, it seems package requires R 4.1. However, there are a few issues while installing R 4.1 (Pre-release) for the window. Do you have any suggestions?

zhiiiyang commented 3 years ago

@amarinderthind, the description lists the R version to be >=3.6. If you can't install it from Bioconductor due to the lower R version, you can also try devtools::install_github("Nanostring-Biostats/NanoStringNCTools")

https://github.com/Nanostring-Biostats/NanoStringNCTools/blob/master/DESCRIPTION#L10

amarinderthind commented 3 years ago

Hi! Sorry to bother you. I can't find a proper document, particularly how to interpret the geometric mean of the housekeeping plot. If it fails, does it mean hk genes frequently detected below the Limit of detection (LOD)? And in this case, i might be changing the hk genes, or if not, then I should exclude the sample with flags.

NicoleEO commented 3 years ago

Hi @amarinderthind, please refer to our support site for assay questions. Our FAQ page, https://www.nanostring.com/support/documentation/knowledge-base-faqs/#data-analysis-and-normalization-general, may be of interest. Feel free to reach out to our support group if you have additional questions: support@nanostring.com.