New releases of R are made very regularly (approximately once a month), as R is actively beingimproved all the time. It is worthwhile installing new versions of R regularly, to make surethat you have a recent version of R (to ensure compatibility with all the latest versions ofthe R packages that you have downloaded).
Genefilter R Download For Windows
The instructions above are for installing R on a Windows PC. If you want to install Ron a computer that has a non-Windows operating system (for example, a Macintosh or computer running Linux,you should download the appropriate R installer for that operating system at -project.org andfollow the R installation instructions for the appropriate operating system at -project.org/doc/FAQ/R-FAQ.html#How-can-R-be-installed_003f).
After the installation of MetaboAnalyst on Glassfish, make a port transfer to ensure you could access the MetaboAnalyst on browsers of windows. You need to know the local IP address of both your host and virtual machine(VM).
Usage Summary Text FileThis file is used by the native aracne2 binaries compiled from C++ source to provide ARACNe2 usage summary. Please copy this file to the same directory as the binary (This can be ignored if the entire source distribution is downloaded)
Some Bioconductor packages will not install by running the biocLite() command. In that case you can always install them from source. In this case you go to the Bioconductor page of the package you wish to instal, as an example we take the Biostrings package (allthough it installs fine using the biocLite() command. How to install this package from source ?Scroll down the Bioconductor page to the Package Archives section
Select the file that corresponds to your operating system, e.g. for windows the zip file
Download the file to your computer and use the following command to install it:install("C:\\path_to_the_file\\Biostrings_2.36.0.zip", repos = NULL, type="source")
Drug IC50 values for docetaxel, bortezomib and erlotinib were downloaded from the CGP website ([52]; accessed August 2013). The raw CGP gene expression microarray data (CEL files) were downloaded from ArrayExpress under accession number E-MTAB-783. These data were preprocessed using the robust multi-array average algorithm (implemented by the rma() function in the affy [53] library in R). This algorithm does background correction, quantile normalization and median-polish summarization in one step. For summarization, we used the updated probeset annotation chip definition file (CDF) provided by BrainArray (version 17.0.0 for Affymetrix HT Human Genome U133A arrays, probesets mapped to Entrez gene IDs). We followed the same set of steps to preprocess the docetaxel, cisplatin and erlotinib/sorafenib clinical trial gene expression data (using the appropriate BrainArray CDF file in each case). The bortezomib expression data were obtained directly from GEO using the getGEO() function implemented in the R library GEOquery [54]. All in vivo drug response data were obtained from GEO or directly from the relevant publication.
The data were first prepared as described above. Next, we divided the cell line training data into sensitive (15 samples) or resistant (55 samples) groups and fitted a logistic ridge regression model using the logisticRidge() function from the R package ridge. Again, the ridge regression tuning parameter was automatically selected. As this implementation of logistic ridge regression is extremely computationally intensive, we implemented a feature selection step, where only the 1,000 genes that were most differentially expressed between the 15 sensitive and 55 resistant samples were fitted in the model. These genes were selected using t-tests, specifically using the rowttests() function in the R library genefilter [56]. This step enables a standard desktop computer to fit a model in approximately ten minutes (as opposed to days). Once the model is fitted, it is applied to the homogenized gene expression data from the clinical trial, using the predict.logisticRidge() function, which calculates the predicted log-odds of drug sensitivity.
Participants are encouraged to check this webpage before the coursebegins and download the files, images and further material here.If possible having a laptop with the released version of R (1.6.2) andthe released version of Bioconductor (1.1) (for the Bioconductor tutorials)will be helpful.
Biobase: data structures and operations on data structures
Annotate: the general approach to dealing with annotation
getting annotation for your experiment
creating hypertext reports for colleagues
genefilter: setting specific filtering criteria
finding genes with interesting patterns
geneplotter: creating heat maps
plotting chromosomal location
The locations of datasets used in this study are listed under Declarations. Previously generated bulk RNA-seq datasets [33] were downloaded, trimmed using Trimmomatic [45], and aligned using the two-pass STAR alignment method [46].
Once you carry out your pkgutil trickery, you can go ahead and download the *.pkg of the R version you want to install and install it like you normally would. If you momentarily open RStudio, you should see that it prints out the new version!
This example uses data from the microarray study of gene expression in yeast published by DeRisi, et al. 1997 [1]. The authors used DNA microarrays to study temporal gene expression of almost all genes in Saccharomyces cerevisiae during the metabolic shift from fermentation to respiration. Expression levels were measured at seven time points during the diauxic shift. The full data set can be downloaded from the Gene Expression Omnibus website, =GSE28.
The .biom and sample data files are also provided online (ftp), and a useful way to download and import into phyloseq directly from the ftp address in the following example code. This is an example in which we download a zip file with both biom- and qiime-formatted data, unzip it in a temporary directory from with in R, import the relavant files using phyloseq importers, and then delete the temporary files. This code should be platform independent, but occasionally there are finicky Windows issues that arise.
That was prune_taxa, applicable when we know (or can provide) the OTU IDs of the OTUs we want to retain in the dataset, or a logical vector with the same length as ntaxa reseulting from a test (useful for genefilter orgenefilter_sample results (see next section)).
This tool takes after the genefilter function from the genefilter package, but emphasizes within-microbiome conditions. The following code illustrates . The function topp is a filter function that returns the most abundant p fraction of taxa. The filterfun_sample function takes one or or more functions like topp and binds them in order to define a filtering protocol function, in this case called: f1. This function, f1, is then passed to genefilter_sample along with the dataset that is going to be pruned as well as a value for A, the number of samples in which an OTU must pass the filtering conditions.
Installers are offered for both Mac (OSX 10.8+) and 64bit Windows operating systems. After downloading the appropriate installer for your system, simply run that EXE or DMG file, and follow the instructions given, in order to put the SeqGeq software platform onto your machine. 2ff7e9595c
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