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tutorial [2013/03/30 10:51] sotacam |
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| ====== NOISeq Tutorial ====== | ====== NOISeq Tutorial ====== | ||
| - | 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/release/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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| - | - Install NOISeq Bioconductor package (see [[downloads|Downloads]]) and load it: ''library(NOISeq)''. | ||
| - | - Download the zip file containing the R scripts for NOISeqBIO (from [[downloads|Downloads]]) and unzip it. | ||
| - | - 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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| - | - 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. | ||
tutorial.1364637068.txt.gz ยท Last modified: 2013/03/30 10:51 by sotacam
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