erccSpikeConcentration: erccSpikeConcentration

Description Usage Arguments Details Value See Also


Various data related to ERCC spikes


  erccSpikeConcentration(file = "")



File name or URL where to find the ‘cms_095046.txt’ text file. Defaults to the current URL on the Thermo Fisher website.


In quantitative transcriptome analysis, we often add synthetic RNA to the reaction for quality control and normalisation, and the External RNA Controls Consortium (ERCC) spikes are a popular choice, available commercially from Invitrogen (now Thermo Fisher). In the commercial product, the spikes have different concentrations, covering six orders of magnitude. These concentrations are given in a text file on the vendor's webiste, and I do not know if the file is freely redistributable, hence this function to retreive the data from the Internet or a local file.


A data frame representing the file ‘cms_095046.txt’ from the vendors website.

The original column names are ‘Re-sort ID’, ‘ERCC ID’, ‘subgroup’, ‘concentration in Mix 1 (attomoles/ul)’, ‘concentration in Mix 2 (attomoles/ul)’, ‘expected fold-change ratio’, ‘log2(Mix 1/Mix 2)’, but this not fit well for a R data frame. Therefore, they are renamed as: ‘sortID’, ‘erccID’, ‘subgroup’, ‘concMix1’, ‘concMix2’, ‘FC’, ‘log2FC’.

See Also


charles-plessy/smallCAGEqc documentation built on May 13, 2019, 3:31 p.m.