Significance analysis of microarrays applied to the ionizing radiation response. Presented by Wenlei Liu Department of Health Evaluation Sciences September 19, 2004. Goal. Differential Analysis of Microarray data :
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Significance analysis of microarrays applied to the ionizing radiation response
Presented by Wenlei Liu
Department of Health Evaluation Sciences
September 19, 2004
Differential Analysis of Microarray data :
Individually identifying genes differentially expressed between two conditions
Study the transcriptional response of lymphoblastoid cells to ionizing radiation (IR).
Two cell lines (1 & 2) were used. Allow cell lines to grow in unirradiated state (U) or in an irradiated state (I) 4 hours after exposure to a modest dose of 5 Gy of ionizing radiation (IR). Divide RNA samples into two parts and performed two independent hybridizations, A and B.
Eight chips– U1A, U1B, U2A, U2B,
I1A, I1B, I2A, I2B.
Compare SAM with
Fold change method –
gene (i) is significant if r(i) > R or < 1/R
Pairwise fold change –compute pairwise fold change using four data sets in state U and state I. A gene is significant if 12 of 16 pairings satisfied the above criteria.
Diagnosis of multiple cancer types by shrunken centroids of gene expression
Errors in the Biopsy Diagnosis of Cancer can lead to:
C(x) = k, where
xij denotes the expression of genes i=1, 2, …, p and samples j=1, 2, ..n. k indexes the cancer classes.
Shrink each dik towards zero, giving dik’ and new shrunken centroids
For gene i, if dik’=0 for all k, then for all k. Gene i does not contribute to the nearest centroid computation.
was chosen by cross-validation.
For a test sample with expression levels
The discriminant score for class k
where k is the prior probability of class k and k=1. And
Small round blue cell tumors (SRBCT) of childhood.
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