The PhenePlate software

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The PhenePlate software
Instructions Step forward with Page Down or by
mouse click
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To start the PhenePlate software Click on the
PhP icon
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The PhP menu
Read PhP data with a microplate reader - DOS
reading version Installation of reader parameters
for the DOS reading version Windows reading
version (only for certain readers)
Create PhP data from absorbance data and from
scanned images Create PhP data after the last
reading with a microplate reader - OBS! Only
nessecary if you used the DOS reading software
Analysis of PhP data
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Reading menu
Read PhP data with a microplate reader - DOS
reading version Installation of reader parameters
for the DOS reading version Windows reading
version (only for certain readers)
The PhP software only works for certain readers.
See the manual for the PhP software on how to
install and run a microplate reader. If you do
not succeed to install your particular reader for
the PhP software, go back to PhP menu and select
Create PhP data from absorbance data and from
scanned images If you have used a flatbed
scanner for reading plates, go back to PhP menu
and select Create PhP data from absorbance data
and from scanned images
Go to beginning Go to PhP menu
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Data analysis
Either select a PhP data file to be analysed
Or select PhP data from another application(e.g.
Excel) file to be analysed
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The main menu
View and edit data Input more data Save data in a
new file Sort and remove samples Normalise data
Normalisation towards negative control
sample Normalisation towards negative control
test Convert data Convert to -/ values
Clear memory and load new data
Calculate similarities for clustering and
dendrogram presentation Comparison to reference
data Pairwise comparisons of isolates Population
statistics (Diversity, Sp etc) Evaluation of tests
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View and edit data
It is more easy to handle the PhP data in
Microsoft Excel. This can be done by copying the
data to clipboard and then pasting into Excel
Open an Excel sheet
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Paste!
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Creating a reference data file
Selected data can be copied to a database
containing data from reference strains, e.g. of
known species.
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Creating a reference data file
Click Save to save selected samples in the data
base
Compare to reference data Back to main menu
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Add text to sample names
You can add text strings to sample names, e.g to
simplify search for certain samples
XXX
XXX
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Remove tests
Go to beginning Go to main menu
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Sort and remove samples
The samples will be sorted in the same order as
they are selected.Note that samples that are not
selected will be removed from the computer memory
(you can still load them again from the data file)
Go to beginning Go to main menu
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Normalise data
Go to beginning Go to main menu
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Analyse data - clustering
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Analyse data - clustering
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Analyse data - clustering
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Analyse data clustering options
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The dendrogram
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The extended list of types
The list is sorted according to the order of
samples. Click on it to view the list sorted
according to types
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Adding marks and text to the dendrogram
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(No Transcript)
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With Excel, the dendrogram can be combined with
other information on the isolates (e.g. PFGE
patterns, MIC values etc.)
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Presenting several dendrograms on the same page
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Presenting several dendrograms on the same page
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Presenting several dendrograms on the same page
Up to 10 dendrograms per page can be presented
Go to beginning Go to main menu
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Comparisons to reference data
If a reference file has not been created yet,
first make sure that the reference data has been
loaded (if not - select Back to main menu - Data
manager and Input more data - load the file
containing reference data)
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Comparisons to reference data
Prints a list of all similarities above the
selected value
Prints only the reference sample to which the
highest similarity is obtained. Use this option
if you are searching a large data base for one
or a few types
Selected reference samples
The lowest similarity level depends on the
purpose of the comparison- for species
identification, use a lower value (e.g. 0.80)-
for detecting clonal groups, use a higher value
(e.g. 0.95)
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Comparison to reference data
Go to beginning Go to main menu
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Pairwise comparisons of samples
Go to beginning Go to main menu
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Population statistics
A population (of bacteria) in this case may
consist of a sample (e.g. a fecal sample or a
water sample) which has been cultivated on
selective agar media. From these media several
pure colonies are picked and typed with the
appropriate PhP plates. The aim of the population
statistics is to be able to determine the
diversity of the bacterial populations in the
samples, and to determine the similarities
between bacterial populations in different samples
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Select the first isolate in each bacterial
population by clicking on it. Alternatively, add
the digits () to the name the first isolate in
each population (e.g. by using Data manager in
PhPWIN), and click Use pre-defined.
The first isolate in each population will be
marked with an X
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The identity level within each population is
normally determined by the intra assay
reproducibility
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The identity level between populations may be set
lower if isolates from several assays are
compared, and the inter assay reproducibility has
been found to be lower than the intra assay
reproducibility
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Mean and median similaries measure the
similarities between all isolates in two
different compared populations.
Population similarity coefficients, mean and
median similarities may be clustered to yield a
dendrogram showing the relations beween different
populations (samples)
Population similarity coefficients (Sp) measure
the proportion of identical strains in two
different compared populations. It thus reflects
the possible spread of bacterial clones between
the samples
Go to beginning Go to main menu
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This option only needs to be used if you have
measured PhP plates using the old DOS reading
software !
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Transformation of scanned plate images to PhP data
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Either the image can be loaded from a .BMP file
that was created by the scanner. Or load the
image from clipboard. The image must then first
be copied to clipboard using the scanner or
another application software.
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Always click on well A1 in the plate first (no
matter its position in the plate image) !!
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Before proceeding with the first plate.
Select reading no
Type a new file name if it was the first reading
occasion
Select an existing .dta file if it was second and
other reading occasions
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The PhP values are shown. On the first reading
occasions names of samples can be added to the
text box
If the data are not ok, click use new
co-ordinates and reload the same plate (or
another plate) If data are ok, click Save data
Sample 1
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If you want to transform absorbance data.....
Go to beginning Go to main menu
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Select a file that contains absorbance data from
PhP plates.
Select option
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Select reading no
Type a new file name if it was the first reading
occasion
Select an existing .dta file if it was second and
other reading occasions
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No click on the first line in the unconverted
data that displays absorbance values
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Look at the converted data Does it seem to
correspond to data from one plate?
Yes Type the names of the isolates in the text
box (optional)
The conversion settings may be permanented by
selectingChange file layout
Isolate 1
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Go to beginning Go to main menu
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Some useful hints
Go to beginning Go to main menu
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How to transfer data between Microsoft Excel and
PhP
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Excel file with PhP data
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Start the PhP software
Select Load data from clipboard
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Select data in the Excel file to be used. The
last columns must contain the PhP data. Copy to
clipboard
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Go back to PhP software and proceed as usual
Now the data has been loadedand may be used like
any other PhP data
Go to beginning Other useful hints
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How to select the most representative isolates
from common PhP types for saving and further
analysis
Analyse the data, create a dendrogram
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The X in the left column indicate the
isolate(s) that is the most representative for
each type (showing the highest minimum similarity
to other isolates belonging to the same type)
The list is sorted according to the order of
samples. Click on the list to sort it according
to the order in the dendrogram
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Selected isolates
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Selected isolates are picked directly from the
wells in the incubated PhP plates
Go to beginning Other useful hints
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How to select the most representative data from
common PhP types for creating a reference data
base
Analyse the data, create a dendrogram
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The X in the left column indicate the
isolate(s) that is the most representative for
each type (showing the highest minimum similarity
to other isolates belonging to the same type)
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Click on the yellow PhP icon on the bottom menu
bar
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Select a new or existing reference file to save
the selected data in
Click on samples to save in the reference file
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THE END
Go to beginning Other useful hints