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MikeJSeo / SAM

SAM (Significance Analysis of Microarrays) shiny app
https://cran.r-project.org/web/packages/samr/index.html
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log intensity data #31

Open shivabt87 opened 6 years ago

shivabt87 commented 6 years ago

Hi, I am a beginner and want to analyze my differentially expressed gene. So, could you please guide me whether I can upload log scale intensity for analysis in SAM. For my log scale probe/gene intensities; Should I run only those genes/probes to check differential expression that has more than 0.5 interquartile or should I run all probes/genes. If I cannot use log value then what statistics should I follow in selecting the probes/genes in linear scale intensities?

MikeJSeo commented 6 years ago

I think that would be fine.. Just need to select the right response ( I think quantitative). Read the manual posted and read the literature related to SAM!