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The NOISeq tutorial can be downloaded from Bioconductor website. Click [[http://www.bioconductor.org/packages/2.12/bioc/html/NOISeq.html|here]]. | The NOISeq tutorial can be downloaded from Bioconductor website. Click [[http://www.bioconductor.org/packages/2.12/bioc/html/NOISeq.html|here]]. | ||
- | In NOISeq package, you can find not only the method to compute **differential expression** between two experimental conditions from RNA-seq data, but also other functions in order to learn more about saturation, contamination or other biases in your data as well as to explore the differential expression results. | + | In NOISeq package, you can find not only the methods NOISeq and NOISeqBIO to compute **differential expression** between two experimental conditions from RNA-seq data, but also other functions in order to learn more about saturation, contamination or other biases in your data as well as to explore the differential expression results. |
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- | ====== NOISeqBIO Tutorial ====== | ||
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- | Please, follow these instructions to run NOISeqBIO: | ||
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- | **1)** Install NOISeq Bioconductor package (see [[downloads|Downloads]]) and load it: ''library(NOISeq)''. | ||
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- | **2)** Download the zip file containing the R scripts for NOISeqBIO (from [[downloads|Downloads]]) and unzip it. | ||
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- | **3)** To load the NOISeqBIO functions in R from your working directory: | ||
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- | # Remember you have to change this path if you are not in the same directory: | ||
- | > mypath = "NOISeqBIO_v00" | ||
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- | > source(file.path(mypath, "auxiliar.R")) | ||
- | > source(file.path(mypath, "MDbio.R")) | ||
- | > source(file.path(mypath, "allMDbio.R")) | ||
- | > source(file.path(mypath, "noiseqbio.R")) | ||
- | > source(file.path(mypath, "classes.R")) | ||
- | > source(file.path(mypath, "normalization.R")) | ||
- | > source(file.path(mypath, "fewreplicates.R")) | ||
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- | **4)** Read your data as in NOISeq (see the following example with Marioni's data) to convert them to a NOISeq object: | ||
- | > data(Marioni) | ||
- | > mydata = readData(data = mycounts, factors = myfactors) | ||
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- | Follow this example of application of NOISeqBIO with your own data: | ||
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- | > mydata = readData() # as in NOISeq (please go to the Tutorial for more information) | ||
- | > myresults = noiseqbio() | ||
- | > myq = 0.95 # Cutoff for the probability of differential expression (1-FDR) | ||
- | > mydeg = | ||
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- | Please, note that you can choose the same normalization procedures as in NOISeq. |