[BioC] edgeR topTags output (logFC)

[Gordon K Smyth]

Dear Susan,

> Date: Mon, 26 Aug 2013 18:28:03 -0700 (PDT)
> From: "Susan [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, smbush at ucdavis.edu
> Subject: [BioC] edgeR topTags output (logFC)
>
>
> I'm just wanting to confirm my understanding of the edgeR topTags() 
> output.  I'm using a design matrix with many coefficients (76 genotypes, 
> 2 treatments[sun, shade]).
>
> 1) In the topTags output, I am looking at logFC which represents the 
> estimated or predicted means -- NOT coefficients, correct?

Incorrect.  As the abbreviation suggests, logFC gives you 
log-fold-changes.  logFC are indeed coefficients, not group means.

> 2) I have selected one parental genotype to be my reference genotype, 
> and I am comfortable interpreting the logFC values for the other 
> genotypes as comparisons to this genotype.  I have selected one 
> treatment as the reference (sun).  When I see the logFC values for 
> 'trtshade', I assume this is also in comparison to the reference 
> genotype in the reference treatment.

Yes, assuming that trt is what you have called the treatment factor, then 
trtshade would the coefficient estimating the log-fold-change between the 
shade and sun treatments.

> My question is about looking at 'geno2.trtshade' values - are these 
> values in comparison to 'trtshade' or 'geno2' or the reference 
> genotype/reference treatment values?

Without knowing what model you have fitted, or which coefficients you have 
tested for, it is impossible to tell.

Best wishes
Gordon

> For example:  this is calling glmLRT with coef = grep("trt", colnames(Design)) to identify treatment effects
>
>           Row.names       logFC.trtsha    logFC.genoIL1.1.trtsha   logCPM        LR        PValue           FDR
> 1 Solyc08g078300.2.1    0.9440264           -0.379030370 4.207443 1135.8061 1.450273e-188 1.637938e-184
> 2 Solyc06g060830.2.1    0.9630343            0.038988710 4.511893 1095.1525 2.539194e-180 1.433883e-176
> 3 Solyc06g067910.2.1    1.2468599           -0.096499016 4.795789 1040.5813 2.722511e-169 1.024935e-165
> 4 Solyc06g008580.2.1    1.1500683           -0.451731914 3.300982  696.1677 6.043868e-101  1.706486e-97
> 5 Solyc07g017600.2.1    0.5026292            0.007208458 5.209938  694.2070 1.451776e-100  3.279271e-97
> 6 Solyc10g083760.1.1   -0.2877568            0.045952894 7.033394  651.8629  2.232759e-92  4.202796e-89
>
> Thanks so much!
>
>
> -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C            LC_COLLATE=C         LC_MONETARY=C        LC_MESSAGES=C        LC_PAPER=C
> [8] LC_NAME=C            LC_ADDRESS=C         LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ggplot2_0.9.3.1 reshape_0.8.4   plyr_1.8        edgeR_3.2.3     limma_3.16.4
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-26        RColorBrewer_1.0-5 colorspace_1.2-2   dichromat_2.0-0    digest_0.6.3       grid_3.0.1         gtable_0.1.2       labeling_0.1
> [9] munsell_0.4        proto_0.3-10       reshape2_1.2.2     scales_0.2.3       stringr_0.6.2      tools_3.0.1


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