fitsod {gcExplorer}R Documentation

E. coli Fermentation Data

Description

E. coli Fermentation Fit Data Object containing M-values, P-values, GeneNames and Links zu NCBI. Output of limma function write.fit with links to NCBI added for each gene.

Usage

data(fitsod)
data(hsod)
data(gobp)

Format

A data frame with 4368 observations on the following variables.

A
a numeric vector giving the mean A-values
Coef.stress3A
a numeric vector for each coefficient giving the estimated coefficient for a particular gene for the contrast to the reference
Coef.stress3B
a numeric vector for each coefficient giving the estimated coefficient for a particular gene for the contrast to the reference
Coef.stress3C
a numeric vector for each coefficient giving the estimated coefficient for a particular gene for the contrast to the reference
Coef.stress3F
a numeric vector for each coefficient giving the estimated coefficient for a particular gene for the contrast to the reference
Coef.stress4
a numeric vector for each coefficient giving the estimated coefficient for a particular gene for the contrast to the reference
Coef.stress4A
a numeric vector for each coefficient giving the estimated coefficient for a particular gene for the contrast to the reference
Coef.stress5A
a numeric vector for each coefficient giving the estimated coefficient for a particular gene for the contrast to the reference
Coef.stress6
a numeric vector for each coefficient giving the estimated coefficient for a particular gene for the contrast to the reference
t.stress3A
a numeric vector giving the t-statistic to the coefficient estimate
t.stress3B
a numeric vector giving the t-statistic to the coefficient estimate
t.stress3C
a numeric vector giving the t-statistic to the coefficient estimate
t.stress3F
a numeric vector giving the t-statistic to the coefficient estimate
t.stress4
a numeric vector giving the t-statistic to the coefficient estimate
t.stress4A
a numeric vector giving the t-statistic to the coefficient estimate
t.stress5A
a numeric vector giving the t-statistic to the coefficient estimate
t.stress6
a numeric vector giving the t-statistic to the coefficient estimate
p.value.stress3A
a numeric vector giving the corresponding p-value
p.value.stress3B
a numeric vector giving the corresponding p-value
p.value.stress3C
a numeric vector giving the corresponding p-value
p.value.stress3F
a numeric vector giving the corresponding p-value
p.value.stress4
a numeric vector giving the corresponding p-value
p.value.stress4A
a numeric vector giving the corresponding p-value
p.value.stress5A
a numeric vector giving the corresponding p-value
p.value.stress6
a numeric vector giving the corresponding p-value
F
a numeric vector giving the overall F-statistik
F.p.value
a numeric vector giving the corresponding F-p-value
Genes.Block
first block position of the gene
Genes.Row
first row position of the gene
Genes.Column
first column position of the gene
Genes.GeneName
Short genename
Genes.ID
Gene ID
Genes.AccessionReference
Blattner numbers
Genes.Status
status of the gene: always gene
links
link to NCBI

Details

The data set hsod is a filtered subset of the original data. It contains 527 differentially expressed genes at the 8 time points. The vector bn_hsod contains the corresponding identifiers which can be used to search for functional groups in the data set gobp. links_hsod contains the corresponding links to the NCBI database.

gobp is a data set listing functional groups to gene identifiers. The data set consists of 8726 observations, the first column gives the gene identifier, the second column gives the gene name and the third column gives the functional group.

References

Duerrschmid, K., Reischer, H., Schmidt-Heck, W., Hrebicek, T., Guthke, R., Rizzi, A., Bayer, K. (2008). Monitoring of transcriptome and proteome profiles to investigate the cellular response of E. coli towards recombinant protein expression under defined chemostat conditions. Journal of Biotechnology 135, 34–44.

Examples

data(fitsod)

[Package gcExplorer version 0.9-1 Index]