Settings:
---------
Input files:
Zip file containing the Affymetrix arrays (.CEL files): example_set2.zip
Dataset description file: description_set2.txt
Samples ordered by group in the QC plots
Results sent by email to this address: magali.jaillard@maastrichtuniversity.nl
Indicators and plots asked:
Sample quality: RNA degradation.
Hybridization quality: Pos/Neg control distribution, Controls profile and boxplot.
Signal distribution: Boxplot (raw), Density histogram (raw), Boxplot(norm), Density histogram (norm).
Intensity-dependent bias: MA-plot (raw), MA-plot (norm)
Spatial bias: Array layout reference plot, Pos/Neg Center Of Intensity, 2D image of raw data, 2D image of weights, 2D image of residuals, 2D image of residual signs.
Probe-set homogeneity:NUSE,RLE.
Array correlation: Correlation plot (raw), PCA analysis (raw), Hierachical clustering (raw), Correlation plot (norm), PCA analysis (norm), Hierachical clustering (norm). (Clusters computed Pearson and ward).
Pre-processing:
Method for the normalization: RMA.
You choose to use a custom annotation file (CDF): REFSEQ applied to Hs.
R command:
affyAnalysisQC(\'-dexample_set2_2011-04-12_15-38_17.zip\', \'-gdesc_example_set2_2011-04-12_15-38_17.txt\', \'-G\', \'-e\', \'-n\', \'-H\', \'-x\', \'-y\', \'-X\', \'-Y\', \'-k\', \'-K\', \'-jdataset\',
\'-F\', \'-N\', \'-R\', \'-W\', \'-q\', \'-Q\', \'-u\', \'-a\', \'-c\', \'-t\', \'-o\', \'-C\', \'-T\', \'-O\', \'-vPearson\', \'-wward\', \'-l\', \'-LREFSEQ\', \'-SHs\', \'-zRMA\', \'-Jdataset\',
\'-Aexample_set2_2011-04-12_15-38_17\')
Standard output:
----------------
[1] "Parameters have been registered"
[1] "Zip file: example_set2_2011-04-12_15-38_17.zip"
[1] "Raw data ready to be loaded in R"
[1] "Raw data have been loaded in R"
Script run using R version 2.12.2
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
[1] "Libraries have been loaded"
[1] "Functions have been loaded"
current cdf environment loaded: HuGene-1_0-st-v1
The arrays are determined to contain perfect match probes only
[1] "Graphs ready to be computed"
[1] " plot degradation plot"
[1] " plot pos & neg control distribution"
[1] " plot control profiles and/or boxplots"
[1] " plot boxplot for raw intensities"
[1] " plot density histogram for raw intensities"
[1] " MA-plots for raw intensities"
[1] " plot array reference layout"
[1] " Pos/Neg COI"
[1] " Fit a probe level model (PLM) on the raw data"
[1] " 2D virtual images"
[1] " NUSE boxplot"
[1] " RLE boxplot"
[1] " Correlation plot of raw data"
[1] " PCA analysis of raw data"
[1] " Hierarchical clustering of raw data"
[1] "Change CDF before pre-processing"
[1] "hugene10stv1_Hs_REFSEQ"
The downloaded packages are in
‘/tmp/Rtmpgp7186/downloaded_packages’
current cdf environment loaded: hugene10stv1_Hs_REFSEQ
[1] "Pre-processing is running"
Background correcting
Normalizing
Calculating Expression
[1] " plot boxplot for normalized intensities"
[1] " plot density histogram for normalized intensities"
[1] " MA-plots for normalized intensities"
[1] " Correlation plot of normalized data"
[1] " PCA graph for normalized data"
[1] " Hierarchical clustering of normalized data"
[1] "Saving normalized data table"
[1] "Normalized data table: RMANormData_example_set2.txt"
Warning and error messages:
---------------------------
Loading required package: methods
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation('Biobase')' and for packages 'citation(pkgname)'.
Attaching package: 'affyPLM'
The following object(s) are masked from 'package:stats':
resid, residuals, weights
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object(s) are masked from 'package:Biobase':
combine
The following object(s) are masked from 'package:utils':
object.size
Users are warned that some or all of the manufacturer supplied files
that this package is based on have been labeled as unsupported by
their sources
trying URL 'http://brainarray.mbni.med.umich.edu/bioc/src/contrib/hugene10stv1hsrefseqcdf_14.0.0.tar.gz'
Content type 'application/x-gzip' length 3450869 bytes (3.3 Mb)
opened URL
==================================================
downloaded 3.3 Mb
* installing *source* package ‘hugene10stv1hsrefseqcdf’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (hugene10stv1hsrefseqcdf)