Northern said its services between Leeds and Bradford and Leeds and Ilkley were disrupted due to the weather, with Network Rail engineers on site.
LNER advised its passengers not to travel to stations north of York.
In Leeds, more than 2,000 households had their power supplies restored after an outage was reported in the West Park and Cookridge areas at around 07:30 GMT.
The amber weather warning is in place until 21:00 GMT on Friday, while the yellow weather warning, which covers most of South Yorkshire, Leeds, Wakefield, York and Tadcaster, is in place until midnight.
The Met Office has advised people to prepare for potential power cuts and for those in coastal areas to be conscious of large waves during stormy weather.
Listen to highlights from West Yorkshire on BBC Sounds, catch up with the latest episode of Look North or tell us a story you think we should be covering here, external.
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