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raw_data_viewer [2008/02/18 08:20]
dmontaner
raw_data_viewer [2017/05/24 10:36] (current)
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 +====== Raw Data Viewer ====== 
 +
 +This module of [[Babelomics]] is intended for the **visualization of raw data**. It is a tool complementary to the [[Normalization|Normalization]] module of [[Babelomics]]. Both tools work over the same [[raw data]] and have a similar [[normalization#data_input|input requirements]].
 +
 +Select the [[Affymetrix]] or the [[twocolor|TwoColors]] button in the form in order to indicate which platform you are analyzing. If you are normalizing a two color platform then you also need to indicate the **Array type** you are using. Selected plots will be displayed in png format.
 +
 +
 +
 +===== Affymetrix raw data plots =====
 +
 +  * **Box-plot**: displays [[Box-plots]] for each of the arrays in your raw data. Just [[pm|perfect match probes]] are used.
 + 
 +  * **PM and MM distributions**: displays //histograms// of the perfect match and mis-match probes for each of the arrays in your raw data.
 +
 +  * **RNA digestion**: a line is displayed for each array aiming to detect possible RNA degradation. Within each probe-set, probes are numbered directionally from the 5' end to the 3' end. Within each array, probe intensities are averaged by probe number, across all genes in the array. These means are represented with a line for each chip.
 +
 +  * **MA plot**: displays [[maplot|MA-plots]] of each of the arrays against a pseudo-median reference computed across all arrays in the raw data.
 +
 +  * **Raw image**: represents the raw data mimicking scanner image.
 +
 +
 +===== Two color arrays raw data plots =====
 +
 +  * **Box-plot**: Log-ratios of the **red** -[[Cy5]]- [[foreground]] channel over the **green** -[[Cy3]]- [[foreground]] channel (i.e. [[mvalues|M-values]]) are displayed in a [[Box-plot]] for each array.
 + 
 +  * **MA plot**: displays [[maplot|MA-plots]] of each of the arrays.
 +
 +  * **Density**: displays density plots of each of the foreground channels in the microarray.
 +
 +  * **Printip**: print-tip loess curves are displayed over an [[maplot|MA-plot]] for each of the print-tip blocks in the array. Cannot be applied to microarray platforms which do not have a print-tip structure like [[Agilent]] for instance.
 +
 +  * **Foreground vs. Background plot**: displays [[foreground]] versus [[background]] intensities for each array.
  
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