Babelomics tutorial
http://wikis.babelomics.org/babelomicstutorial/
2024-03-19T12:39:41+00:00Babelomics tutorial
http://wikis.babelomics.org/babelomicstutorial/
http://wikis.babelomics.org/babelomicstutorial/lib/tpl/arctic/images/favicon.icotext/html2013-01-07T15:11:57+00:00fgarciadata_upload - [Upload your data]
http://wikis.babelomics.org/babelomicstutorial/data_upload?rev=1357571517&do=diff
Babelomics has a unique data entry point in its Upload Menu.
[Upload link]
By accessing to this form you will be able to upload any datafile you want to analyze using Babelomics. One single file can be uploaded at a time.
[Upload form]
* Click on Choose File button and browse the directory where you have saved your file. This file can be a unique file or a compressed archive containing several files, generaly raw data files. Babelomics can read .zip and .tar.gz. When uploading raw …text/html2012-10-02T08:38:28+00:00fgarciaid_converter
http://wikis.babelomics.org/babelomicstutorial/id_converter?rev=1349167108&do=diff
Dealing with identifiers coming from many databases is a major problem when merging information or when analysing data at the functional level. The process of identifiers conversion into many databases has been implemented in Babelomics as an independent tool, the ID converter.text/html2012-04-17T11:00:30+00:00pablosidebar
http://wikis.babelomics.org/babelomicstutorial/sidebar?rev=1334660430&do=diff
* Babelomics
* Babelomics Team
* Publications
* History
* Resources
* Example Datasets
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* User account
* Data administration
* Project administration
* Getting Data from GEO and Array Express
* Uploading Data
* Data Typestext/html2012-01-27T15:03:35+00:00fgarciaedit_data
http://wikis.babelomics.org/babelomicstutorial/edit_data?rev=1327676615&do=diff
* In the main menu go to Processing data and then click on the Edit button.
[Edit data link]
* Select the DataSet in which you want to enter new variables and press in Create new variable.
[Select dataset]
* The following step is to insert a name for the new variable and assign a value type. Value types can be: CATEGORICAL, NUMERIC or STRING.
(e.g. Phenotypic variables have, frequently, CATEGORICAL values, such as 'control' and 'disease'. This kind of information is used afterwar…text/html2011-09-21T15:50:41+00:00fgarciababelomics
http://wikis.babelomics.org/babelomicstutorial/babelomics?rev=1316620241&do=diff
Babelomics is an integrated web-based pipeline for the analysis of genomic data. It is specially appropriated for the analysis of high-throughput data like those generated in microarray studies. Babelomics stands for Gene Expression Pattern Analysis Suite. The suit includes tools for normalization, clustering, differential gene expression, class prediction and functional annotation.text/html2011-06-06T12:31:09+00:00aamadozbiclustering - [Filter]
http://wikis.babelomics.org/babelomicstutorial/biclustering?rev=1307363469&do=diff
Different genes have different expression levels according to their specific function at each condition. Biclustering identifies groups of genes with similar expression patterns under a specific subset of conditions. These conditions may correspond to different time-points, for example in times series expression data.text/html2011-05-23T08:16:27+00:00aamadozclustering - [Distance functions]
http://wikis.babelomics.org/babelomicstutorial/clustering?rev=1306138587&do=diff
Class discovery or unsupervised problems
There are two classes of problems extensively addressed in the microarray field: supervised and unsupervised problems. We talk about unsupervised problems when we do not know beforehand (or it is not part of our hypothesis) the structure of classes that our data set has. Typical examples of unsupervised problems would be the definition of the molecular variability of a population of bacteria, or finding the groups of co-expressing genes. In none of these…