Beruflich Dokumente
Kultur Dokumente
version 6.1
BioRssay
version 6.1
Using
BioRssay
To
use
the
script
you
must
have
the
R
software
installed
on
your
computer
(http://cran.r-
project.org/).
Then
you
need
to
download
the
script
and
the
examples
files
(zip
file)
from
http://www.isem.univ-montp2.fr/recherche/equipes/genomique-de-
ladaptation/personnel/labbe-pierrick/.
Open
the
script
in
a
text
editor.
Then
open
R
and
copy-paste
the
script.
Open
your
data
file.
When
the
script
is
finished
running,
the
graphs
and
results
files
are
in
the
same
directory
as
your
data
file.
Tip:
clear
the
console
between
two
runs
of
the
script
(control
+
l),
it
increases
the
speed
Data
preparation
Prepare
a
text
file
(.txt)
with
at
least
4
columns
(see
Example1.txt,
Example2.txt
and
Example
3.txt):
-
one
column
"souche"
(=
strain)
for
each
strain
tested,
-
one
column
"dose"
for
each
dose
in
each
replicate.
Note:
if
you
have
controls
(i.e.
replicates
without
the
active
substance),
enter
them
with
a
dose
equal
to
0.
You
must
have
controls
for
each
strains,
even
if
you
want
to
analyze
them
in
one
strain
only.
-
one
column
"tot"
for
the
total
number
of
larvae
tested
at
each
dose
in
each
replicate,
-
one
column
"morts"
(=
dead)
for
the
number
of
dead
larvae
at
each
dose
in
each
replicate.
Additionally,
you
can
add
a
"color"
column
if
you
wish
to
customize
the
graphs.
In
this
column
just
choose
an
integer
for
each
strain
tested,
starting
from
1
to
the
number
of
strains
tested
(n).
Note
that
the
color
are
those
of
the
palette
rainbow
in
R
(rainbow(10)
if
the
n<10,
rainbow(n)
if
n>10).
Tip:
use
the
following
command
in
R
to
see
the
corresponding
colors:
plot(1:10,
col=rainbow(10))
Similarly,
you
can
also
add
a
"symbol"
column
if
wish
to
customize
the
data
point
symbol.
In
this
column
just
choose
an
integer
for
each
strain
tested.
From
version
5.1:
you
can
now
indicate
whether
you
want
to
use
one
of
the
strains
as
the
reference
to
compute
the
resistance
ratios.
Just
add
"-ref"
at
the
end
of
the
strain
name
in
you
file.
If
no
strain
presents
the
"-ref"
extension,
the
strain
with
the
minimum
LD50
will
be
used
as
reference.
You
can
have
any
other
column
you
want:
for
example
you
can
copy
your
data
for
a
large
spreadsheet,
as
long
as
you
don't
use
the
previous
labels.
Examples
Example
1
In
this
example
there
are
3
strains,
for
7
doses
and
2
replicates
each.
Note
that
a
color
column
is
provided.
All
controls
are
below
5%
mortality.
KIS
is
used
as
the
reference
(indicated
as
KIS-ref
in
the
data
file).
version 6.1
After
running
the
script,
you
would
have
the
following
report:
-
For
each
strain
you
have
first
the
LD50
and
LD95
and
their
upper
and
lower
limits
(95%
CI),
then
the
slope
and
intercept
of
the
regression
(with
their
standard
error),
the
heterogeneity
(h)
and
the
g
factor
("With
almost
all
good
sets
of
data,
g
will
be
substantially
smaller
than
1.0
and
seldom
greater
than
0.4."
Finney,
1971).
-
The
result
of
the
chi
test
(Chi(p))
is
then
indicated
to
judge
whether
the
data
are
well
fitted
to
the
regression
or
not:
here
all
the
p-values
are
over
0.05
so
the
fits
are
acceptable).
This
is
more
reliable
in
version
6.1.
-
Finally
the
resistance
ratios
are
indicated
for
LD50
and
LD95
(RR50
and
RR95).
-
As
there
are
3
strains,
the
script
first
tests
whether
they
are
all
similar
(i.e.
equivalent
to
1
strain)
or
not
(3
strains
vs
1
strain).
Here,
the
test
is
highly
significant,
some
strains
are
thus
different
in
terms
of
resistance.
-
To
test
which
are
different
or
not,
pairwise
tests
are
then
performed
and
reported
here
in
a
table.
KIS
strain
is
different
from
DZOU
and
from
DZOU2
strains
(p
=
8.36E-61,
and
p=3.15E-48).
DZOU
and
DZOU2
are
not
different
(p
=
0.264).
-
The
significant
values
remain
significant
after
Bonferroni
correction
(in
the
table
below
there
is
a
1
in
the
bonferroni
column).
The
corresponding
graphs
are
showed
below,
with
the
colors
corresponding
to
those
indicated
in
the
data
file.
The
first
shows
the
regression
with
the
data
points;
the
second
one
shows
only
the
regressions.
From
version
6.1
you
get
two
additional
graphs
with
the
95%
CI
of
the
regression.
99
DZOU
99
DZOU
DZOU2
DZOU2
KISref
KISref
95
95
90
90
80
80
70
70
60
60
50
50
40
40
30
30
20
20
10
10
5
5
1
1
10
10
10
10
10
10
Dose(mg.L )
Dose(mg.L )
Mortality (%)
Mortality (%)
version 6.1
99
99
DZOU
DZOU2
KISref
DZOU
DZOU2
KISref
95
95
90
90
80
80
70
Mortality (%)
Mortality (%)
60
50
40
30
20
70
60
50
40
30
20
10
10
103
102
101
1
Dose(mg.L
103
102
101
Dose(mg.L1)
Example
2
In
this
example
there
are
2
strains,
for
7
doses
and
2
replicates
each.
Note
that
no
color
column
is
provided.
Some
controls
present
a
mortality
>
5%.
After
running
the
script,
you
would
have
the
following
report:
-
For
each
strain
you
have
first
the
LD50
and
LD95
and
their
upper
and
lower
limits
(95%
CI),
then
the
slope
and
intercept
of
the
regression
(with
their
standard
error),
the
heterogeneity
(h)
and
the
g
factor
("With
almost
all
good
sets
of
data,
g
will
be
substantially
smaller
than
1.0
and
seldom
greater
than
0.4."
Finney,
1971).
-
The
result
of
the
chi
test
(Chi(p))
is
then
indicated
to
judge
whether
the
data
are
well
fitted
to
the
regression
or
not:
here
all
the
p-values
are
over
0.05
so
the
fits
are
acceptable).
This
is
more
reliable
in
version
6.1.
-
Finally
the
resistance
ratios
are
indicated
for
LD50
and
LD95
(RR50
and
RR95).
-
As
there
are
2
strains,
no
pairwise
test
is
required.
Thus,
the
script
only
tests
whether
they
are
all
similar
(i.e.
equivalent
to
1
strain)
or
different
(2
strains
vs
1
strain).
Here,
the
test
is
highly
significant;
the
two
strains
are
thus
different
in
terms
of
resistance.
-
In
this
dataset,
the
control
showed
a
mortality
>
0.05,
so
the
data
are
corrected
using
Abbott's
formula.
An
estimation
of
the
mortality
in
the
controls
is
provided:
about
2%
in
DZOU,
and
9%
in
KIS.
Both
estimations
have
converged
(0
in
convergence
column).
Note
that
if
convergence
is
not
0,
you
should
try
to
run
the
script
again,
usually
is
solves
the
problem.
The
corresponding
graphs
are
showed
below,
with
the
default
colors.
The
first
shows
the
regression
with
the
data
points;
the
second
one
shows
only
the
regressions.
From
version
6.1
you
get
two
additional
graphs
with
the
95%
CI
of
the
regression.
version 6.1
99
DZOU
KIS
99
95
90
80
Mortality (%)
80
70
60
50
40
30
20
70
60
50
40
30
20
10
5
DZOU
KIS
95
90
10
103
102
101
1
Dose(mg.L
99
103
101
Dose(mg.L
DZOU
KIS
99
95
DZOU
KIS
95
90
90
80
80
70
60
50
40
30
20
70
60
50
40
30
20
10
5
102
1
Mortality (%)
Mortality (%)
Mortality (%)
10
1
103
102
Dose(mg.L1)
101
103
102
101
1
Dose(mg.L
Example
3
In
this
example
there
are
2
strains,
for
7
doses
and
2
replicates
each.
Note
that
no
color
column
is
provided.
All
controls
are
below
5%
mortality.
One
strain
does
not
fit
a
linear
regression.
After
running
the
script,
you
would
have
the
following
report:
-
For
each
strain
you
have
first
the
LD50
and
LD95
and
their
upper
and
lower
limits
(95%
CI),
then
the
slope
and
intercept
of
the
regression
(with
their
standard
error),
the
heterogeneity
(h)
and
the
g
factor
("With
almost
all
good
sets
of
data,
g
will
be
substantially
smaller
than
1.0
and
seldom
greater
than
0.4."
Finney,
1971).
version 6.1
-
The
result
of
the
chi
test
(Chi(p))
is
then
indicated
to
judge
whether
the
data
are
well
fitted
to
the
regression
or
not:
here
the
p-value
for
KIS
is
over
0.05
so
the
fit
is
acceptable,
but
the
p-value
for
DZOU
is
below
0.05
so
the
data
differ
significantly
from
the
predicts
of
the
regression.
Here
it
is
a
classic
case
of
a
mix
between
two
types
of
individuals,
some
susceptible,
some
resistant.
This
is
more
reliable
in
version
6.1.
-
Finally
the
resistance
ratios
are
indicated
for
LD50
and
LD50
(RR50
and
RR95).
-
As
there
are
2
strains,
no
pairwise
test
is
required.
Thus,
the
script
only
tests
whether
they
are
all
similar
(i.e.
equivalent
to
1
strain)
or
different
(2
strains
vs
1
strain).
Here,
the
test
is
highly
significant.
However,
as
the
DZOU
strain
does
not
fit
a
linear
regression,
the
test
cannot
be
interpreted.
The
corresponding
graphs
are
showed
below,
with
the
default
colors.
The
first
shows
the
regression
with
the
data
points;
in
the
second
one,
as
the
data
of
one
strain
(DZOU)
were
significantly
different
from
the
regression
predicts,
only
the
data
are
shown
for
the
corresponding
strain,
not
the
regression.
From
version
6.1
you
get
two
additional
graphs
with
the
95%
CI
of
the
regression.
99
DZOU
DZOU
99
KIS
KIS
95
95
90
90
80
80
70
70
60
60
50
50
40
40
30
30
20
20
10
10
5
5
1
1
10
10
10
10
10
10
10
10
Dose(mg.L )
Dose(mg.L )
DZOU
DZOU
99
99
KIS
KIS
95
95
90
90
80
80
70
70
60
60
50
50
40
40
30
30
20
20
10
10
5
5
1
1
10
10
10
10
10
10
10
10
Dose(mg.L )
Dose(mg.L )
Mortality (%)
Mortality (%)
Mortality (%)
Mortality (%)
version 6.1
References
Abbott,
WS
(1925).
A
method
of
computing
the
effectiveness
of
an
insecticide.
J.
Econ.
Entomol.;
18
:
265-267.
Finney
DJ
(1971).
Probit
analysis.
Cambridge:
Cambridge
University
Press.
350
p.
Hommel
G
(1988).
A
stagewise
rejective
multiple
test
procedure
based
on
a
modified
Bonferroni
test.
Biometrika
75,
383-6.
Johnson
RM,
Dahlgren
L,
Siegfried
BD,
Ellis
MD
(2013).
Acaricide,
fungicide
and
drug
interactions
in
honey
bees
(Apis
mellifera).
PLoS
ONE
8(1):
e54092.
Robertson,
J.
L.,
and
H.
K.
Preisler.
1992.
Pesticide
bioassays
with
arthropods.
CRC,
Boca
Raton,
FL.