I recently updated my system to the latest aroma, and now something that
worked in the last version is not working now.
I use a script originally from Mark Robinson called doEverything. That
seems just fine, all my usual steps work. I can use plotRle and plotNuse
just fine. When I get to the ArrayExplorer section in order to try to
generate array images of the residuals I get the no png error. I also tried
this after doing library(grDevices) to make sure png() was available.
> library(grDevices)
> rs <- e.AndersonRat1$res
> ae <- ArrayExplorer(rs)
> setColorMaps(ae, c("log2,log2pos,rainbow"))
> process(ae, interleaved="auto")
Interleaving image...
z:
num [1:1050, 1:1050] NA NA NA NA NA NA NA NA NA NA ...
- attr(*, "...instantiationTime")= POSIXct[1:1], format: "2011-02-24
10:50:17"
Infering horizontal, vertical, or no interleaving...
hOdd=0.81
hEven=0.81
hRatio=0.0013
vOdd=0.81
vEven=0.81
vRatio=-2.5e-05
what: none
Infering horizontal, vertical, or no interleaving...done
Interleaving image...done
Error in loadNamespace(name) : there is no package called 'png'
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8
LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] abind_1.1-0 limma_3.6.6 preprocessCore_1.12.0
affyio_1.18.0 Biobase_2.10.0 aroma.affymetrix_2.0.0
[7] aroma.apd_0.1.8 affxparser_1.22.0 R.huge_0.2.2
aroma.core_2.0.0 aroma.light_1.18.3 matrixStats_0.2.2
[13] R.rsp_0.4.2 R.cache_0.4.0 R.filesets_0.9.2
digest_0.4.2 R.utils_1.6.2 R.oo_1.7.5
[19] EBImage_3.6.0 affy_1.28.0 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] tools_2.12.1
I would be very grateful for any suggestions or help,
Thanks,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D. University of Washington
Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/members_fc_bioinfo.html
http://staff.washington.edu/~dbeyer
*******************************************************************************
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