[BioC] Multiple comparisons: inquiries on level factors and wording used in resultsNames

[Yoong [guest]]

Hi Mike, 

Sorry to bother you about multiple comparisons again. 

I’d like to inquire about certain wording/phrases used in resultsNames(dds) to better understand the types of comparisons made. 

My questions will be based on the output from the resultsNames(dds4): please see the output. I am not entirely clear about the codes/wording used in the description. For example, the word ‘versus’ used in genotypeC_vs_GenotypeB. Is it implying a comparison of tempHigh versus tempLow between genotypeC versus genotype B for all time points? Another confusing word is period. What does it mean genotypeC.TempHi? Is it implying a comparison of genotype C at tempHi over all time points? How should I interpret all these comparisons?

Also, when I called results(dds), you said it would compare effect of tempHi versus tempLow over GenotypeB, over all time points. If I’d like to make multiple comparisons of tempHi versus tempLow for more than 2 genotypes simultaneously against each other, why is it still important to set a base level? If I set a base level, all the comparisons will be made against the base level, not against each other. To illustrate, I am interested in comparing genotypeA, genotypeB, and genotypeC. If I set genotypeA as my base level, I will be comparing genotypeB and genotypeC against genotypeA. I won’t be making any comparison genotypeB to genotypeC. Please explain more on the level of factors. I am a little bit confused with that in terms of multiple comparisons. 

To remind you again, here’s my experimental design:
Genotypes: 4 different genotypes
Timepoint: 3 different timepoints (6h, 12h, and 24h)
Temperature: Low and high temperatures
3 biological replicates for each condition.

Thank you for your quick responses!

Regards,
Yoong


 -- output of sessionInfo(): 

dds3 = DESeqDataSetFromMatrix(countData = allData, colData = colData, design = ~genotype+time+temp+genotype:temp+ time:temp)

dds4= DESeq(dds3,betaPrior=FALSE)

resultsNames(dds4)

"Intercept"            "genotypeC_vs_ GenotypeB "  "genotypeA_vs_ GenotypeB"
"genotype_GenotypeD_vs_GenotypeB"  "time_24h_vs_12h"        "time_6h_vs_12h"
"temp_TempHi_vs_TempLow"      "genotypeC.TempHi" "genotypeA.TempHi"
"genotypeD.TempHi" "time24h.TempHi"       "time6h.TempHi"

results(dds4,name="temp_TempHi_vs_TempLow")

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