GADL1 {SARP.compo} | R Documentation |
Gene expression change in bipolar disorder
Description
This data set gives the mRNA quantification of a few genes compared between bipolar disorder patients and healthy volunteers.
Usage
data(GADL1)
Format
A data frame with 13 columns and 56 rows. Each row gives the quantification results, expressed in amounts:
Groupe | factor | The group label, Ctrl for healthy volunteers and BPD for bipolar disorder patients |
Phenotype | factor | the subgroup label, C for healthy volunteers, NR for patients not responding to treatment and R for patients responding to treatment |
Sample | factor | the sample unique identifier |
All other columns are numeric and give the amount, in arbitrary unit, of mRNA of the corresponding gene. The column name gives the name of the gene and the dilution used for the quantification. hprt and sdha are used as reference genes.
Source
Original data communicated by the authors of the experiment.
Examples
data( GADL1 )
# Optimal cut-off for ten genes and alpha = 0.05
# is around 0.22
# First step, is there differences between healthy subjects
# and patients ?
#
M.m <- creer.Mp( d = GADL1, noms = names( GADL1 )[ -c( 1:3 ) ],
f.p = student.fpc, v.X = 'Groupe' )
# 2) L'arbre associƩ
# [reference gene for plotting purpose]
n.ref <- grep( 'HPRT|SDHA', names( GADL1 ), value = TRUE )
plot( arbre.Mp( M.m, reference = n.ref ),
seuil.p = c( 0.218, 0.207, 0.230 ) )
# 3) Le graphe pour le seuil optimal
# => only IGF1 seems to behave differently
# (but it has missing values, so interpretation is difficult)
plot( grf.Mp( M.m, reference = n.ref, p = 0.22 ) )
# Second step, is there differences between patients
# that respond or not respond to treatment?
d.R <- GADL1[ which( GADL1$Groupe == 'BPD' ), ]
M.R <- creer.Mp( d = d.R, noms = names( GADL1 )[ -c( 1:3 ) ],
f.p = student.fpc, v.X = 'Phenotype' )
# 2) L'arbre associƩ
plot( arbre.Mp( M.R, reference = n.ref ),
seuil.p = c( 0.218, 0.207, 0.230 ) )
# 3) Le graphe pour le seuil optimal
# => no sign of any difference
plot( grf.Mp( M.R, reference = n.ref, p = 0.22 ) )
[Package SARP.compo version 0.1.8 Index]