- Corrected a bug in positiveQC(), which caused it to calculate different positive scale factors from normalize_pos_control(); the second was confirmed to be correct.
- runLimmaAnalysis now allows optional arguments, which are passed to limma::lmFit.
- The codeclass.retain option now allows runLimmaAnalysis() to be run using a CodeClass/CodeClasses specified by the user, instead of automatically removing non-endogenous genes. See help(runLimmaAnalysis) for details.
- processNanostringData() can now handle a vector of .rcc files, in addition to the previous options for loading NanoString data.
- We're published in Bioinformatics! CITATION file updated.
- In addition to ruv::RUVIII, the RUVSeq::RUVg method can now be used for data normalization. Options have also been added to allow tuning of the parameters for these methods. More details are provided in the vignette.
- A csv or txt file containing a design matrix can be input as a 'sampleTab' in processNanostringData(). This facilitates easier differential expression analysis with more complex models, and an example has been added to the vignette.
- Various other improvements to vignette.
- NanoTube can now process zipped and tarred (.zip or .tar) directories, as well as gzipped (.gz) RCC files, such as those downloaded from GEO in many cases.
- Corrected a bug that caused NanoTube not to recognize reporters labeled as "Endogenous1", "Endogenous2", etc. as Endogenous.
- When processing a folder containing RCC files, processNanostringData() now ignores filenames not ending in "RCC" (case-insensitive).
- Corrected a bug that in read_cpdb_sourceDBs() and read_cpdb_tab() that sometimes led to the data being misread.
- Pre-release version