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SubtitleTextAlt-splicing dialog, select factors and alt-splicing factors
AnchorNameAlt-splicing

 Only and only one alt-splicing factor needs to be selected from the ANOVA factors. The ANOVA model performed is based on the factors specified in the dialog,  the transcript ID and transcript ID interaction with alt-splicing factor effects are added automatically into the model: 

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Suppose there is an experiment designed to detect transcripts showing differential expression in two tissue groups: liver vs muscle. The alt-splicing ANOVA dialog allows you to specify the ANOVA model that is tissue, the alt-splicing factor is chosen from the ANOVA factor(s), so the alt-splicing factor is also tissue (Figure 1). Click Next to setup the comparisons (Figure 2)

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SubtitleTextAlt-splicing ANOVA comparisons setup dialog
AnchorNameAlt-splicing-contrast

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The subgroups of the alt-splicing factor will be displayed in the left panel; click to select a subgroup name and move it to one of the panels on the right. The fold change calculation on the comparison will use the group in the top panel as numerator, and the group in the bottom panel as denominator. Click on Add comparison button to add on comparison to the comparisons table.

ANOVA advanced options

Click on the Configure to customize Advanced options (Figure 3)

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SubtitleTextConfiguring advanced options when running alt-splicing ANOVA
AnchorNameAlt-splicing-adv

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Low-expression feature and Multiple test correction sections are the same as the matching GSA advanced option, see above GSA advanced options

Report option

    • User only reliable estimation results: There are situations when a model estimation procedure does not fail outright, but still encounters some difficulties. In this case,  it can even generate p-value and fold change on the comparisons, but they are not reliable, i.e. they can be misleading. Therefore, the default of Use only reliable estimation results is set Yes.

    • Data has been log transformed with base: showing the current scale of the input data on this task.

Alt-splicing ANOVA report

The report format is the same as ANOVA report 

 

Additional assistance

 https://documentation.partek.com/

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