If this error message occurs prior to ChipST2C installation, then you will need to download and install the Microsoft .NET Framework 1.1 Redistributable Package . ChipST2C is solely based on the “next-generation technology” from Microsoft contained in its .NET Framework. The .NET Framework is currently being developed and is therefore not available on all Windows XP operating systems. Eventually, .NET Framework will be bundled in all future versions of the Windows operating system.
Change the screen resolution to show more pixels, i.e., Start --> Control panel --> Display --> Settings --> 1024 x 768 pixels. VGA and SVGA monitors are not supported.
In
order to prevent errors during the FILE OPEN procedure, it is recommended that
you save an Excel spreadsheet as tab-delimited text file within
Excel.
Refer to the first section in the User's Guide on saving data to a
tab-delimited text file.
If you can’t seem to prevent errors during file open, then look for double quotes “” or blank records in the middle of the Excel file. If a genename is missing in the genename column, then an error will occur. If you don’t know a genename, either drop the record, or place something in the genename column such as “Unk” or “N/A” for these kinds of genes.
This is likely caused by having commas somewhere in the genenames. If you replace commas with semicolons ";" this problems should not occur.
Cluster analysis is a multivariate statistical method that can easily require heavy computational resources. In medicine, it is typical for statisticians to work with data representing only a few hundred patients and maybe 5-10 variables in the final analysis. However, most genomic data sets contain data for thousands of genes which presents a tremendous challenge for any desktop PC.
The reason why you have a memory shortage is as follows. Consider the distance (in km) between 100 cities. There is a "pairwise" distance between city 1 and 2, 1 and 3,...,1 and 100, pairwise distance between city 2 and 3, 2 and 4,...,2 and 100, and so on. The total number of pairwise distances between these cities is N=(#cities)(#cities-1)/2, or (100)(99)/2 =4,950. Distances are also used in cluster analysis. Consider the Affymetrix U95A Human GeneChip® with 12,626 genes. The number of distances between these 12,626 genes is N=(12,626)(12,626-1)/2 =79,701,625. During computation in the computer, each of these 79,701,625 distances requires 4 bytes of storage in random access memory (RAM) for single-precision and 8 bytes for double-precision. Under single-precision, this amounts to 318,806,500 bytes or 319 megabytes (MB) of RAM. Under double precision, this amounts to 637,613,000 bytes or 634 megabytes (MB) of RAM. If your computer has 64 or 128 megabytes of RAM, you would not be able to do the calculations necessary for cluster analysis of the U95A chip. This is why the recommended amount of RAM is 512 MB.
A general rule of thumb for single-precision floating point math is that if you need to cluster X genes, then the minimum amount of bytes of RAM needed is 2X^2=2(X)(X). To convert this to megabytes (MB), divide by 1,000,000 or one million. By default, ChipST2C uses double precision for all variables and arrays, except for the distance array which is in single-precision.