validTreetype: Validate Tree Type

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Validate tree type for corresponding data type.

Usage

validTreetype(treetype, datatype)

Arguments

treetype	tree type.
datatype	data type.

Details

Every ROOT tree has an extension, which describes the type of data stored in this tree. For example, ‘TestA1.cel’ is the tree name that stores the CEL-file data for ‘TestA1.CEL’.

Trees with datatype="scheme" have the following extensions:
scm: scheme tree containing (x,y)-coordinates and mask for UNIT_ID.
idx: unit tree containing UnitName (i.e. probeset id), NumCells, NumAtoms, UnitType, for UNIT_ID.
prb: probe tree containing probe sequences.
ann: transcript annotation tree.
anx: exon annotation tree; exon arrays only.
anp: probeset annotation tree; exon arrays only.
cxy: coordinate tree containing CLF-file information; exon arrays only.
exn: exon tree; exon arrays only.
pbs: probeset tree; exon arrays only.

Trees with datatype="rawdata" have the following extensions:
cel: data tree containing CEL-file data.

Trees with datatype="preprocess" have the following extensions:
int: intensity tree containing background-corrected intensities.
sbg: background tree containing MAS4 sector background levels.
wbg: background tree containing MAS5 weighted sector background levels.
rbg: background tree containing RMA background levels.
gbg: background tree containing GC-content background levels.
cmn: cell tree containing preprocessed intensities using algorithm ‘mean’.
cmd: cell tree containing preprocessed intensities using algorithm ‘median’.
clw: cell tree containing preprocessed intensities using algorithm ‘lowess’.
css: cell tree containing preprocessed intensities using algorithm ‘supsmu’.
cqu: cell tree containing preprocessed intensities using algorithm ‘quantile’.
dc5: detection tree containing MAS5 detection call and p-value.
dab: detection tree containing DABG detection call and p-value.
amn: expression tree containing expression levels computed with ‘arithmetic mean’.
gmn: expression tree containing expression levels computed with ‘geometric mean’.
wmn: expression tree containing expression levels computed with ‘weighted mean’.
wdf: expression tree containing expression levels computed with ‘weighted difference’.
adf: expression tree containing expression levels computed with ‘average difference’.
tbw: expression tree containing expression levels computed with ‘tukey biweight’.
mdp: expression tree containing expression levels computed with ‘median polish’.
rlm: quality tree containing expression levels, NUSE, RLE computed with ‘median polish’.
res: residual tree containing the residual SE and the model fit weights.
brd: border tree containing border intensities, mean border intensities and COI.

Trees with datatype="normation" have the following extensions:
tmn: expression tree after normalization using algorithm ‘trimmed mean’.
med: expression tree after normalization using algorithm ‘median’.
ksm: expression tree after normalization using algorithm ‘kernel smoother’.
low: expression tree after normalization using algorithm ‘lowess’.
sup: expression tree after normalization using algorithm ‘supsmu’.
qua: expression tree after normalization using algorithm ‘quantile’.
mdp: expression tree after normalization using algorithm ‘median polish’.

Value

Returns the valid treetype, otherwise an error message is returned.

Note

Not all tree types are used in the current package.

Author(s)

Christian Stratowa

See Also

getDatatype, type2Exten

Examples

validTreetype("prb", "scheme")
validTreetype("cel", "rawdata")
validTreetype("tbw", "preprocess")

xps documentation built on Nov. 8, 2020, 6 p.m.