8.1 Microarray experiments  (Page 2/4)

As a demonstration, view the Stanford Microarray Database website. Under the Public Data section, click on the "Public Login" link. Limit the data set search to the organism Arabidopsis thaliana and the author Gutierrez. Click on the button entitled "Display data", and a table of microarray datasets should be returned. Choose one of the experiments, making note of the Experiment ID number from the table and select the clickable image icon. (There is a legend for the icons at the top of the web page, if there is uncertainty as to which is the clickable image icon.) This yields the qualitative visualization of the microarray experiment, as described previously in this module. Take a look at the array image and note that it is difficult to draw many conclusions fromthis kind of visualization.

Click on one of the individual spots in the microarray grid. This will open a new window that contains a close up of the individual spot and all the experimental information about that spot.

Return to the table of Arabidopsis thaliana data sets and forExperiment ID #11374, select the "Data" icon, which is the first icon under the "Options" column. Next to "Sort By", select "Log(base2) of R/G NormalizedRatio (Mean)", and "Descending". Under "Display:", click on "Spot", then scroll down and hold down the control key (or the apple key on macintoshes) while selecting "Log(base2) ofR/G Normalized Ratio (Mean)". (The control key allows selection of additional choices without deselecting the previous choice.) Accept the default values for allremaining options and select "Display" at the bottom of the page. Recall that the data are converted to numbers representingthe fluorescence intensity of red dye, green dye, and the ratios of red to green. Scientists commonly use a log transformation of the ratio data, because thelogs are more mathematically tractable in reference to statistical analysis. The results page will show the top ranking spots from this chip, ranked from highest log red/green value to lowest.

Use the browser's back button to go back and select new data for display. Chage the sortingselection to R/G Normalized (Mean), in descending order. under the "Display:" window select "Spot", then scroll down and hold down the control key while selecting "R/G Normalized (Mean)".