Fixed vignette
Added initial support to Generic Arrays
Using BiocGenerics definition of normalize
Removed dependency on RConverters.h
Improved results by getProbeInfo();
fitPLM, coefs and resids are now Defunct. Use fitProbeLevelModel, coef and residuals respectively. 'coef' and 'residuals' follow the standards used elsewhere in R;
Fixed problem caused by the fact that oligoClasses had its own annotation() method when BiocGenerics added a new one;
Several fixes to probe selector, allowing 'target' to be used;
PA Calls didn't know about target;
New getProbeInfo() function added, to simplify probe selection without using SQL.
New fitProbeLevelModel() function added. It allows probe-level models ('plm' and 'medianpolish'), which can be used for QC.
fitPLM, coefs and resids are now Deprecated. Use fitProbeLevelModel, coef and residuals respectively. 'coef' and 'residuals' follow the standards used elsewhere in R.
Now using foreach for parallelization.
Addressed issue in which probes without chr info would be removed from pmChr, leading to results whose dimensions did not match PM matrix (on TilingFeatureSet).
pmStrand() now available for Affy-Tiling arrays (by Kristof De Beuf);
Fixed message method when normalizing with large dataset support;
Using NEWS.Rd;
New summarization methods are available: PLM, PLMr, PLMrr and PLMrc. These are implemented in the basicPLM function and also available through the summarize() interface (method=c('plm', 'plmr', 'plmrr', 'plmrc'));
fitPLM(), NUSE() and RLE() are now available;
Presence/Absence calls are available through paCalls();
MAplot method with advanced options;
'pm<-', 'mm<-', 'bg<-' now work with ff_matrix replacements;
boxplot() now uses the correct (default) ylim if transfo != log2;
Fixed documentation for hist(), boxplot(), fitPLM();
Fixed image for PLMset on NimbleGen arrays;
Added support to read gzipped XYS files directly.
Added information for citation.
Added getNetAffx method to retrieve NetAffx annotation for Exon ST and Gene ST arrays.
Reading in uncompressed XYS files is much faster than in 1.12.2.
Added vignette for Exon/Gene ST arrays (rma and NetAffx annot)
Fixed bug in boxplot / hist / MAplot
Fixed issue that would appear with GeneFeatureSet objects, in which it selections like obj[c(2, 2, 1),] would generate invalid GeneFeatureSet objects
Fixed bugs in image / bg / bgindex / bgSequence for Exon and Gene arrays (due to changes in annotation)
Added date/time of scan (for XYS/CEL files) to the protocolData slot. For 1 channel applications, the field is called 'dates'; for 2 channel apps, there are 2 fields: 'dates1' and 'dates2'
New method, runDate(), to extract scan dates from FeatureSet objects
New vignette structure: Vignette 1: Overview (with multiple examples) Vignette 2: Expression (NimbleGen data) Vignette 3: SNP Genotyping (Affymetrix)
Uses Imports rather than Depends. Users must explicitly load Biobase, affyio, preprocessCore if they need functions from these packages.
Revised man page for rma.
Support to large datasets via ff package. The user should load the ff package in order to use this feature. Files used by ff are saved to getwd(), unless the user changes the standard path.
Support to parallel computing via snow package. The user should load *both* ff and snow in order to use the parallel features implemented in the package (backgroundCorrect, normalize, summarize, rma, normalizeToTarget). Cluster variable should be set as options(cluster=makeCluster(...)).
seqColors and darkColors, respectively, generate a vector of sequential colors (in blue) and (qualitative) dark colors (based onn Dark2 from RColorBrewer).
plotM method for SnpSuperSet (plot genotype clusters).
getAffinitySplineCoefficients estimates the affinity spline coefficients.
getBaseProfile estimates and optionally plots sequence effect like gcrma.
Fixed definition for probeNames() for Exon/Gene arrays. (Mikhail Pachkov)