Description Usage Arguments Details Value See Also
Various data related to ERCC spikes
1 | erccSpikeConcentration(file = "http://tools.thermofisher.com/content/sfs/manuals/cms_095046.txt")
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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’.
loadMoiraiStats
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