Description Usage Arguments Details Value Author(s) References
Function to make all boxplots required for quality control.
1 |
ds |
ds object created with aroma.affymetrix and the function AffymetrixCelSet() from the .CEl files and the cdf file. |
ds.N |
Aroma affymetrix ds.N object with the normalized data from .CEL files using RMA and quantile normalization. |
plmTr |
plmTr object obtained with the ExonRmaPlm function in aroma.affymetrix() package. |
picname |
Character with the output file name. |
labels |
Optional. Vector with sample names. Samples are in the same order as in the ds object. Default get sample names from the ds object. |
conditions |
Optional, vector with sample condition. IMPORTANT conditions are in the order corresponding to mixedsort(labels). |
colors |
Optional, vector with the colours corresponding to each condition with the order mixedsort(samplename). |
raw.bp |
Plot boxplots with raw data at log2 scale. Default TRUE. |
RMA.bp |
Plot boxplots with normalized log2 data. Default TRUE. |
RLE |
Plot boxplots with relative log expression values (RLE). Default TRUE. |
NUSE |
Plot boxplots with normalized unscaled standard errors (NUSE). Default TRUE. |
resDir |
Output results directory. Default is ResultsDir. |
This function outputs boxplots for quality assessment in microarray data using objects obtained with aroma.affymetrix package pre-processing. A boxplot with raw data, and a boxplot with Normalized data. Additionally reports relative log expression values (RLE), and normalized unscaled standard errors (NUSE).
This function outputs plots in .png format in the resDir directory.
Magdalena Arnal Segura <marnal@imim.es>
H. Bengtsson, K. Simpson, J. Bullard & K. Hansen. aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report #745, Department of Statistics, University of California, Berkeley, February 2008.
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