Graph Irregularities

This Tuesday (April 14th), I went to RPI to analyze data from another microarray affinity experiment. Affinity is the attraction to a substance, in this case a labeled protein. We used two different blocking buffers in this experiment. On one microarray, we used the BSA (bovine serum albumin) that we usually use with the microarrays. On the other microarray, we used a crude mixture (protein broth) from the company whose protein we are trying to purify, which contains contaminants as well as the protein of interest. Both of these microarrays were tested in concentrations from 1 nM to 3.5 nM. We graphed the data as intensity vs. concentration, where high intensity meant high affinity toward the printed peptide. The expected intensity vs. concentration graph would look like the graph below.

However, I looked through all of the graphs and found irregularities like the ones shown below. The third irregularity is especially strange because the intensity is very high at low concentrations, but very low at high concentrations.

After I finished recording the irregularities in the graphs, I looked at the kD values for the same experiment. I looked at each peptide sequence in relation to its position on the protein, and recorded the high and low kD values for each region.

Also, there was a vendor fair in our building today! We took a break to go look at the new technology, including movers, shakers, and much more. Overall, it was a lot of fun!