Overview

High-Throughput GoMiner™ generates files that are useful for cluster analysis. The purpose of these instructions is to facilitate construction of clustered image maps (CIMs) using CIMminer so that users can both replicate the cluster images found in the High-Throughput GoMiner manuscript, and create similar CIMs constructed from their own data.

Browser Requirements

• CIMminer works best with Internet Explorer. However, all of the steps here can be done with most major browsers.

Specific Instructions for Figure 3 of the High-Throughput GoMiner manuscript

We refer to CIMs similar to Figure 3 as “trinary” because they contain exactly three values. In particular, the values are -1, 0, and 1.

1. Start with the input file, CHANGEDGENESFILE.change.gce.updown.CIM which is described in Output Files.
2. If you are using a Mac, make sure the file ends in '.txt'.
3. On the following section, select the following clustering options, as shown here:
   Clustering
   
4. This will generate an initial CIM. Select Colors and adjust the all of the display options for Colors, Page Layout and Axes, and then press Redraw.
   1. Colors
      
   2. Page Layout
      
   3. Axes
      
5. This will generate a new CIM. Save this CIM as .gif. Right-click (Control Click on a Mac) to reveal menu and select “Download Image to Disk.” This menu item may be phrased differently on your browser.
   

Specific Instructions for Figure 4 of the High-Throughput GoMiner manuscript

We refer to CIMs similar to Figure 4 as “continuous” because the entries can assume any floating point values. In this particular instance, the values are all non-negative.

1. Start with the input file, total.txt.change.series.CIM which is described in Output Files.
2. If you are using a Mac, make sure the file ends in '.txt'.
3. On the following section, select the following clustering options, as shown here:
   Clustering
   
4. This will generate an initial CIM. Select Colors and adjust the all of the display options for Colors, Binning, Page Layout and Axes, and then press Redraw.
   1. Colors
      
   2. Binning
      
   3. Page Layout
      
   4. Axes
      
5. This will generate a new CIM. Save this CIM as .gif. Right-click (Control Click on a Mac) to reveal menu and select “Download Image to Disk.” This menu item may be phrased differently on your browser.
   

Pitfalls

• If you get the error message: "There was an error processing your files in R, The cluster distance you selected is not defined for your dataset. For example, you selected "binary" distance, your dataset is not discrete (character) data," be sure your dataset is appropriate for the distance metric you selected. Examine your data and remove the offending row or column, and try to generate the CIM again.
• If you get the error message: "Your datafile has an inconsistent number of tab separated values per line," a possible culprit could be extra tabs at the end of your data files. You should not get this error when processing data directly from High-Throughput GoMiner, but it is possible to accidentally introduce this error if you manually edit the cluster data file.

We would like to hear from you. You can reach the team via email.

GoMiner was originally developed jointly by the Genomics and Bioinformatics Group (GBG) of LMP, NCI, NIH and the Medical Informatics and Bioimaging group of BME, Georgia Tech/Emory University. It is now maintained and under continuing development by GBG.

Notice and Disclaimer