normalized | R Documentation |
Function normalize makes all libraries in dataset have the same library size.
normalized(dat, nci, m=0, lg2="no")
dat |
count data of RNA reads. |
nci |
number of columns for the information of genes or isoforms in dataset. |
m |
numeric value for choosing genes or isoforms. If user wants to discard genes or isoforms with mean < 5, then m = 5. The default value is 0. |
lg2 |
logistic value. lg2="yes"indicates that data are transformed in logarithm of 2. |
Due to difference in RNA abstraction between libraries or cell samples or tissues, PCR amounts of RNA libraries would have difference that is not due to biological effects. To correctly compare differential expressisons of genes between conditions or samples, one must should give the same RNA abstraction in all given samples. This is impossible. To address this problem, only one way is to normalize these count data across all given samples so that all experimental samples (libraries) have the same total counts.
output a standard datasheet.
Yuan-De Tan tanyuande@gmail.com
Yuan-De Tan Anita M. Chandler, Arindam Chaudhury, and
Joel R. Neilson(2015) A Powerful Statistical Approach
for Large-scale Differential Transcription Analysis.
Plos One, 10.1371/journal.pone.0123658.
Anders S, Huber W (2010) Differential expression
analysis for sequence count data. Genome Biol,
11: R106.
data(jkttcell) njkttcell<-normalized(dat=jkttcell[1:50,],nci=7)
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