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Old 09-16-2015, 03:51 AM   #1
EVELE
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Location: France

Join Date: Jun 2015
Posts: 9
Default Use of test="Wald" in the results of a time-course experiment

Hi all,

Concerning the example of the manual :
http://bioconductor.org/help/workflows/rnaseqGene/#time
in the "Time Course Experiments" paragraph,

library("fission")
data("fission")
ddsTC <- DESeqDataSet(fission, ~ strain + minute + strain:minute)
ddsTC <- DESeq(ddsTC, test="LRT", reduced = ~ strain + minute)

resultsNames(ddsTC)

## [1] "Intercept" "strain_mut_vs_wt" "minute_15_vs_0" "minute_30_vs_0"
## [5] "minute_60_vs_0" "minute_120_vs_0" "minute_180_vs_0" "strainmut.minute15"
## [9] "strainmut.minute30" "strainmut.minute60" "strainmut.minute120" "strainmut.minute180"

res30 <- results(ddsTC, name="strainmut.minute30", test="Wald")
res30[which.min(resTC$padj),]

## log2 fold change (MLE): strainmut.minute30
## Wald test p-value: strainmut.minute30
## DataFrame with 1 row and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## SPBC2F12.09c 174.6712 -2.601034 0.6314737 -4.11899 3.805364e-05 0.2572426

When should we use the test="Wald" in the results function?

What are the results I get when I write:
res30 <- results(ddsTC, name="strainmut.minute30")
and what is the difference in the results by adding test="Wald"?
res30 <- results(ddsTC, name="strainmut.minute30", test="Wald")?

Thanks in advance for any ideas
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