Download How to Composite Microarray Data Files

DiDonato, Ray 1-2
How to Composite Microarray Data Files
(Sent by B. Methe)
Description of Composite Files:
Information concerning the log2 ratios of the intensity values from the cDNA
representing the wild type and the experiment.
Gives:
1. ORF number
2. Locus ID
3. Name of each ORF followed by a number which indicates the number of hybs
done for that experiment (usually column D).
4. Mean ratio value (usually column E)
5. Standard deviation of mean ratio (usually column F)
6. Log2 ratio from each individual hyb (column G until the end)
1S, 1F labels are not really of importance
1. Track hybridization number and the manner in which experimental and control
cDNA populations were labeled with fluorescent dyes.
2. Used to look for changes in expression that are more likely artifacts due to dye
effects
The log2 ratios across all of the hybs are given as experimental/control
1. Example:
a. For the Fur experiment it is the log2 ratio of the intensity value of the Fur
mutant/intensity of the wt.
b. Do not have to account for the different dye labeling strategies, as already
done.
c. For the Fur mutant you will notice:
d. All negative ratios of the ORF02344 (Fur) indicating down regulation of
that gene in relation to the wild type
e. All positive ratios of the gene such as ORF05444 (a ferrous iron transport
protein) indicating up regulation in the mutant versus the wild type.
2. It is possible that some ratios will be positive in some hybs and negative in others.
a. This is part of the inherent noise in microarrays, so we try to do a lot of
replication.
b. Oftentimes these ratios are close to zero however and reflect that
essentially no change in expression has been observed for that gene under
the conditions tested.
Number (N) column:
The number of good hybs included in the experiment for that gene.
1. Example:
a. A total of six hybs were done for a biological replicate
b. Six would be the maximum number of values (log2 ratios) that would be
recorded for that gene.
c. If for some reason enough spots representing a gene failed the quality
control for one particular hyb then no value is given for that ORF
d. Each gene is replicated multiple times on a slide
e. Shows NaN in that column
DiDonato, Ray 2-2
f. The number five would be in the Number (N) column as only five good
values were used to calculate the mean log2 ratio.