[BioC] Which log2FC to report?

[Gordon K Smyth]

> Date: Tue, 15 Apr 2014 06:50:34 -0700 (PDT)
> From: "Rafael Moreira [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, rafaelmoreira at gmail.com
> Subject: [BioC] Which log2FC to report?
>
>
> Hello community, I'm using DESeq and edgeR to conduct RNA-Seq data analysis.
> I want to get log2FC adjusted for (possible) lane effects. For example, in edgeR I use:
>
> design = model.matrix(~ lane + condition, data=tmp)
> de = DGEList(counts, group=tmp$condition)
> de = calcNormFactors(de)
> de = estimateGLMCommonDisp(de, design)
> de = estimateGLMTrendedDisp(de, design)
> de = estimateGLMTagwiseDisp(de, design)
> fit = glmFit(de, design)
> lrt = glmLRT(fit, coef='conditiontreated')

Yes, this is the right way to test for DE genes for condition adjusted for 
lane effects.  It is also the right way to get the corresponding 
log-fold-changes, although for that purpose the glmLRT() step is not 
needed.

Note that edgeR gives shrunk logFC, and the amount of shrinkage is 
controlled by the prior.count argument to glmFit().  The default is to do 
a minimal but useful amount of shrinkage, which is almost always 
preferable to raw fold changes.

The edgeR User's guide includes two fully worked case studies that are 
very closely analogous to your experiment.  In the oral carcinoma case 
study (Section 4.4), the patients are equivalent to the lane effects in 
your experiment.  In the arabdopsis case study (Section 4.5), the batch 
effects are equivalent to the lane effects in your experiment.

> while in DESeq2, I have:
> rawData <- DESeqDataSetFromMatrix(counts, pd, ~ lane + condition)
> dds <- DESeq(rawData, test='LRT', reduced= ~ lane)
>
>> From the documentation, this seems the right way of getting the DE genes when I want to account for the lane effect. Is this correct? Or would be something like
>
> DESeq(rawData)
>
> sufficient? (and of course getting the results for the proper coefficient)

> Does the same apply for edgeR?

Does what apply to edgeR?

Best wishes
Gordon

> -- output of sessionInfo():
>
> R version 3.0.3 Patched (2014-03-06 r65200)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  splines   stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] DESeq2_1.2.10           RcppArmadillo_0.4.200.0 Rcpp_0.11.1
> [4] GenomicRanges_1.14.4    XVector_0.2.0           IRanges_1.20.7
> [7] BiocGenerics_0.8.0      edgeR_3.4.2             limma_3.18.13
>
> loaded via a namespace (and not attached):
> [1] annotate_1.40.1      AnnotationDbi_1.24.0 Biobase_2.22.0
> [4] DBI_0.2-7            genefilter_1.44.0    grid_3.0.3
> [7] lattice_0.20-29      locfit_1.5-9.1       RColorBrewer_1.0-5
> [10] RSQLite_0.11.4       stats4_3.0.3         survival_2.37-7
> [13] XML_3.95-0.2         xtable_1.7-3

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