[R] Help required with png graphic production as text has shadows?

[Alice Johnstone]

I have produced a series of graphs with the png command, however when I have finally printed these out the black text appears to have a colour shadow with blue or red on either side of the letter.
I tried increasing my res to 1200 and this improved it somewhat, but the text is still not sharp and occassionally these "shadows" will still print.

I initially thought this was an issue with the printer.. But I can produce a pdf image and it is sharp.  However as I have 50+ images I want to include in a word document the pdf files are much too large and was the reason I was using png.

I am using an older version of R, but didn't want to upgrade as this may cause issues with my completed analyses and the potential changes to other functions.

Can someone suggest what it is I have missed?
Thank you very much.

Alice Johnstone

Example code:
Png("volcano.png",units="cm",height=15,width=15,res=1200,pointsize=12)
Volcano2(fit2.eb,coef=2,highlight=5,xlab="log fold change",ylab="log odds",pch=16,cex=0.5, main="Volcano Plot",xlim=c(-2,2))
Dev.off()


> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32

locale:
LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252

attached base packages:
 [1] grid      splines   tools     stats     graphics  grDevices utils
 [8] datasets  methods   base

other attached packages:
 [1] affyQCReport_1.20.0       arrayQualityMetrics_1.8.1
 [3] marray_1.20.0             beadarray_1.10.0
 [5] hwriter_0.93              latticeExtra_0.5-4
 [7] simpleaffy_2.18.0         affyPLM_1.18.0
 [9] preprocessCore_1.4.0      RColorBrewer_1.0-2
[11] vsn_3.8.0                 genefilter_1.22.0
[13] survival_2.34-1           geneplotter_1.20.0
[15] annotate_1.20.0           xtable_1.5-4
[17] lattice_0.17-15           sma_0.5.15
[19] rat2302probe_2.3.0        rat2302cdf_2.3.0
[21] rat2302.db_2.2.5          RSQLite_0.7-1
[23] DBI_0.2-4                 AnnotationDbi_1.4.0
[25] MASS_7.2-44               gcrma_2.14.0
[27] matchprobes_1.14.0        affy_1.20.0
[29] Biobase_2.2.0             limma_2.16.2
[31] gplots_2.6.0              gdata_2.4.2
[33] gtools_2.5.0

loaded via a namespace (and not attached):
[1] affyio_1.10.0      KernSmooth_2.22-22

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