Jose Garcia

Question 1

Which effect has applying log2-transformation on the distributionof the microarray expression raw data?

Answer 1

It makes the distribution of data more similar to a normal distribution centered in “O”, and this will as well facilitate the application of subsequent statistical tests

Question 2

What are housekeeping genes?

Answer 2

Housekeeping genes are generally constitutive genes required for the maintenance of basic cellular function, and are expressed in all cells of an organism under normal and patho-physiological conditions

Question 3

Among the microarray normalization methods that we have described in our lessons, which was the most effective for neutralizing outliers?

Answer 3

Quantile normalization

Question 4

Please enumerate the standard steps followed in microarray analysis

Answer 4

Microarray raw dataset- data transformation- Normalization- quality control- statistical test- phatway analysis

Question 5

What is a principal component analysis (PCA)?

Answer 5

lt is a statistical procedure that converts a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components

Question 6

What is a statistical test?

Answer 6

It is a mathematical method that cantellus if the results we observe are real or just due to chance. Associated with each statistic is a p-value that tells us if something is statistically significant. If someone says the test was statistically significant they mean the results are likely not due to random chance

Question 7

Among the multiple testing correction methods (mtc) we have used, which one results in less false positives and more false negatives?(1) and which one results in more false positives and less false negatives?(2)

Answer 7

1. Bonferroni FWER

2. Benjamini Hochberg FDR