By Rocky S. Tuan
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Additional resources for Recombinant Gene Expression Protocols
Plots show log of ratio ( M = log(chipl/chip2)) versus average log intensity ( A = (log chip1 log chip2)/2) for all genes. + The t-test looks at the mean and variance of the sample and control distributions and calculates the probability that the observed difference in mean occurs when the null hypothesis is true3. When using the t-test it is often assumed that there is equal variance between sample and control. That allows the sample and control to be pooled for variance estimation. If the variance cannot be assumed equal you can use Welch's t-test which assumes unequal variances of the two populations.
Fig. 11 Artist’s illustration of array of 8 nanomechanical cantilevers. Binding of targets leads to bending that is detected by deflection of a laser beam. 5 EXAMPLE: AFFYMETRIX VS. , 2001) performed both cDNA array analysis and Affymetrix chip analysis of human T-cells infected with Human Immunodeficiency Virus (HIV). 12 shows mRNA extracted from the T-cells and visualized with a cDNA array. First, the mRNA was converted to cDNA and then it was labeled with a fluorochrome. We used a red fluorochrome for the mRNA that was extracted from the HIV-infected cells (experiment, sample, or treatment) and we used a green fluorochrome 76 INTRODUCTION TO DNA MlCROARRAY TECHNOLOGY Fig.
Up-regulated genes have a fold change greater than 1 and down-regulated genes have a fold change less than -1. But the scale for down-regulated genes is comparable to the scale for up-regulated genes Both the fold change and Affyfold expressions are intuitively rather easy to grasp and deal with, but for further computational data analysis they are not useful, either because they are asymmetric or because they are discontinuous. For further data analysis you need to calculate the logarithm of fold change.
Recombinant Gene Expression Protocols by Rocky S. Tuan