I am trying to plot unshrunken log2FC in DESeq and get an error that MLE is not a graphic parameter. In fact, plots for shrunken and unshrunken FC look the same.

​
> head(res)
log2 fold change (MAP): condition WEN vs WNN
Wald test p-value: condition WEN vs WNN
DataFrame with 6 rows and 7 columns
                                baseMean log2FoldChange      lfcMLE       lfcSE       stat    pvalue      padj
                               <numeric>      <numeric>   <numeric>   <numeric>  <numeric> <numeric> <numeric>
ENSMUSG00000051951.5/Xkr4   1333.2828047   -0.003633939 -0.08022292 0.028046235 -0.1295696 0.8969070 0.9999026
ENSMUSG00000025900.4/Rp1       0.5336683   -0.006972621 -4.95474964 0.006503632 -1.0721120 0.2836697 0.9999026
ENSMUSG00000025902.7/Sox17   270.7340834   -0.035019526 -0.26573804 0.045634649 -0.7673890 0.4428503 0.9999026
ENSMUSG00000033845.7/Mrpl15  836.9071001   -0.098643864 -0.17786080 0.067020770 -1.4718402 0.1410640 0.9999026
ENSMUSG00000025903.8/Lypla1 1082.8204648   -0.050723134 -0.08167419 0.065420364 -0.7753417 0.4381378 0.9999026
ENSMUSG00000033813.8/Tcea1  2554.7830159   -0.037331591 -0.05395727 0.062261760 -0.5995910 0.5487789 0.9999026​


> DESeq2::plotMA(res,MLE=TRUE,main="unshrunken LFC")
Warnmeldungen:
1: In plot.window(...) : "MLE" ist kein Grafikparameter
2: "MLE" ist kein Grafikparameter 
3: "MLE" ist kein Grafikparameter 
4: In plot.xy(xy, type, ...) : "MLE" ist kein Grafikparameter
5: In axis(side = side, at = at, labels = labels, ...) :
  "MLE" ist kein Grafikparameter
6: In axis(side = side, at = at, labels = labels, ...) :
  "MLE" ist kein Grafikparameter
7: In box(...) : "MLE" ist kein Grafikparameter
8: In title(...) : "MLE" ist kein Grafikparameter




> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DESeq2_1.8.2              RcppArmadillo_0.6.200.2.0 Rcpp_0.12.2               GenomicRanges_1.20.8      GenomeInfoDb_1.4.3        IRanges_2.2.9            
[7] S4Vectors_0.6.6           BiocGenerics_0.14.0      

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2   futile.logger_1.4.1  plyr_1.8.3           XVector_0.8.0        futile.options_1.0.0 tools_3.2.1          rpart_4.1-10         digest_0.6.8        
 [9] RSQLite_1.0.0        annotate_1.46.1      gtable_0.1.2         lattice_0.20-33      DBI_0.3.1            proto_0.3-10         gridExtra_2.0.0      genefilter_1.50.0   
[17] stringr_1.0.0        cluster_2.0.3        locfit_1.5-9.1       nnet_7.3-11          grid_3.2.1           Biobase_2.28.0       AnnotationDbi_1.30.1 XML_3.98-1.3        
[25] survival_2.38-3      BiocParallel_1.2.22  foreign_0.8-66       latticeExtra_0.6-26  Formula_1.2-1        geneplotter_1.46.0   ggplot2_1.0.1        reshape2_1.4.1      
[33] lambda.r_1.1.7       magrittr_1.5         scales_0.3.0         Hmisc_3.17-0         MASS_7.3-45          splines_3.2.1        xtable_1.8-0         colorspace_1.2-6    
[41] stringi_1.0-1        acepack_1.3-3.3      munsell_0.4.2       

Dear Tonja

you'll need a more recent version of DESeq2, the MLE option for plotMA was only introduced in version 1.10.0: https://bioconductor.org/packages/release/bioc/news/DESeq2/NEWS

A workaround seems to be here: plotMA in DEseq2

Kind regards

Wolfgang