Signal intensities (relative mRNA prevalences) and signal detection calls (P, A, or M) for all GeneChip experiments were generated using MAS 5.0 algorithm. For comparative purposes, GeneChip data were scaled globally to a target intensity of 500 for all probe sets on the chip using MAS 5.0 default parameters. Each probe set was manually assigned a consensus detection call based on the MAS 5.0 detection calls of both biological replicates of an RNA sample. Probe sets with same signal detection calls in both biological replicates were assigned consensus detection calls of P, A, or M, respectively. Consensus detection calls are used in the search form:
Depending on the purpose of the analysis, "AND and "OR" are used to get a list of genes of
interest. The figures below are shown the different result using "AND" and "OR" with same selected GeneChip data.
To select multiple experiments, for PC user, press CTRL key and select experiments; for Mac user, press Command/Apple key and select experiments.
The relationship between each criterion box is "AND" relationship. For example, in the first criterion box, the user selects genes present in embryo proper at globular stage; in the second criterion box, genes absent in embryo proper at heart stage. The result will include genes present in embryo proper at globular stage, but absent in embryo proper at heart stage.
The user has to select at least one GeneChip experiment. The default setting for "Relationship between experiments" is "And". The default setting for "Consensus Detection Call" is "Any". And the default setting for "Signal Value" is "Any".
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1. Select the experiment "Soybean array/Soybean/Cotyledon Stage/Embryo Proper" 2. Select the Detection Call as "P(all)" 3. Click Add another set of criteria button to add another criterion |
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4. In the second criterion box, select experiments for all other tissues at cotyledon stage by pressing CTRL key (PC user) or Command/Apple key (Mac user) and selecting experiments at the same time 5. Select the Detection Call as "A" in the second criterion box 6. Click Submit Query button to start the analysis |
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The result will be displayed in a table. The user can download the annotation, GeneChip data, or both
in text format for all matched genes found by clicking the buttons on the right-top corner of the result table.
The user also can click on the probe set ID to view its mRNA profile including:
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1. Select the experiment "Soybean array/Soybean/Cotyledon Stage/Embryo Proper" 2. Select the Detection Call as "P(all)" 3. Click Add another set of criteria button to add another criterion |
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4. In the second criterion box, select the experiments "Soybean array/Soybean/Globular Stage/Embryo Proper" and
"Soybean array/Soybean/Heart Stage/Embryo Proper" by pressing CTRL key (PC user) or Command/Apple key (Mac user) and selecting experiments at the same time 5. Select the Detection Call as "A" in the second criterion box 6. Click Submit Query button to start the analysis |
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The result will be displayed in a table. The user can download the annotation, GeneChip data, or both
in text format for all matched genes found by clicking the buttons on the right-top corner of the result table.
The user also can click on the probe set ID to view its mRNA profile including:
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1. Select the experiment "Soybean array/Soybean/Cotyledon Stage/Embryo Proper" 2. Select the Detection Call as "P(all)" 3. Select the Signal Value as ">" and type in "1000" 4. Click Add another set of criteria button to add another criterion |
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5. In the second criterion box, select the experiments "Soybean array/Soybean/Globular Stage/Embryo Proper" and
"Soybean array/Soybean/Heart Stage/Embryo Proper" by pressing CTRL key (PC user) or Command/Apple key (Mac user) and selecting experiments at the same time 6. Select the Detection Call as "A" in the second criterion box 7. Click Submit Query button to start the analysis |
|
The result will be displayed in a table. The user can download the annotation, GeneChip data, or both
in text format for all matched genes found by clicking the buttons on the right-top corner of the result table.
The user also can click on the probe set ID to view its mRNA profile including:
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1. Select the experiments "Soybean array/Soybean/Cotyledon Stage/Embryo Proper"
and "Soybean array/Soybean/Cotyledon Stage/Endosperm" 2. Select the Relationship between experiments as "Or" 3. Select the Detection Call as "P(all)" 4. Click Submit Query button to start the analysis |
|
The result will be displayed in a table. The user can download the annotation, GeneChip data, or both
in text format for all matched genes found by clicking the buttons on the right-top corner of the result table.
The user also can click on the probe set ID to view its mRNA profile including: