Cc: Microarray time series experiment for Caulobacter crescentus...

In ptest: Periodicity Tests in Short Time Series

Description

In this microarray experiment there are 3062 genes measured every 1 hour. There are 19 is missing gene labels and these have been given labels ORFna1,...,ORFna19. There 310 with duplicate labels. Of these duplicate labels, 295 are duplicated twice, 12 are duplicated 3 times and 3 are duplicated 4 times. Duplicate labels are renamed ORF... to ORF...a and ORF...b etc.

Usage

data(Cc)

Format

Matrix with 3062 rows and 11 columns. Some missing data. Rows and columns are labelled. - attr(*, "dimnames")=List of 2 ..$ : chr [1:3062] "ORF06244a" "ORF03152a" "ORF03156a" "ORF03161a" ... ..$ : chr [1:11] "1" "2" "3" "4" ...

Details

Gene expression from synchronized cultures of the bacterium Caulobacter crescentus (Laub et al., 2000). (Laub et al., 2000) identified 553 genes whose messenger RNA levels varied as a function of the cell cycle but their statistical analysis was not very sophisticated and they probably identified too many genes. Wichert et al. (2004) found that 44 genes were found which displayed periodicity based on the Fisher's g-test using a FDR with q=0.05.

References

Laub, M.T., McAdams,H.H., Feldblyum,T., Fraser,C.M. and Shapiro,L. (2000) Global analysis of the genetic network controlling a bacterial cell cycle Science, 290, 2144-2148.

Wichert,S., Fokianos K. and Strimmer K. (2004) Identifying periodically expressed transcrips in microarray time series data. Bioinformatics, 18, 5-20.

Examples

data(Cc)
qqnorm(colMeans(Cc, na.rm=TRUE))
qqnorm(rowMeans(Cc, na.rm=TRUE))

ptest documentation built on May 2, 2019, 5:58 a.m.