ini.call {xps} | R Documentation |
Computes the Informative/Non-Informative Call for the exclusion of non-informative probe sets.
ini.call(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", weight = 0.5, mu = 0.0, scale = 1.0, tol = 0.00001, cyc = 100, alpha1 = 0.4, alpha2 = 0.6, version = "1.3.1", option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE) xpsINICall(object, ...)
xps.data |
object of class DataTreeSet . |
filename |
file name of ROOT data file. |
filedir |
system directory where ROOT data file should be stored. |
tmpdir |
optional temporary directory where temporary ROOT files should be stored. |
weight |
hyperparameter, usually set to 0.5 for version="1.3.1" and to 8.0
for version="1.3.0" . |
mu |
hyperparameter allowing to correct for potential bias. |
scale |
scaling parameter, usually set to 1.0 for version="1.3.1" and to 2.0
for version="1.3.0" . |
tol |
termination tolerance for EM algorithm. |
cyc |
maximum number of cycles of EM algorithm. |
alpha1 |
a significance threshold in (0,alpha2). |
alpha2 |
a significance threshold in (alpha1,1.0). |
version |
version of original farms package. Currently, version="1.3.1" and
version="1.3.0" are implemented. Default is version="1.3.1" . |
option |
option determining the grouping of probes for summarization, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only. |
exonlevel |
exon annotation level determining which probes should be used for summarization; exon/genome arrays only. |
xps.scheme |
optional alternative SchemeTreeSet . |
add.data |
logical. If TRUE call data will be added to slots data and detcall . |
verbose |
logical, if TRUE print status information. |
object |
object of class DataTreeSet . |
... |
the arguments described above. |
In contrast to mas5.call
this function quantifies the signal-to-noise ratio for
each probe set, as described in Talloen et al. Thus, the returned p-values and detection calls
have a different meaning:
The p-value that is returned estimates the signal-to-noise ratio (SNR):
P-values (SNR) of less than 0.5 indicate that there is more signal than noise and the
corresponding genes are considered to be ‘informative’ for further analysis. In
contrast, values greater than 0.5 indicate ‘non-informative’ genes.
The informative call is computed by thresholding the p-value as in:
call “P” if p-value < alpha1
call “M” if alpha1 <= p-value < alpha2
call “A” if alpha2 <= p-value
Here “P” should be considered as informative “I”, “M” as marginally informative, and “A” as non-informative “NI”.
The defaults for alpha1=0.4
and alpha2=0.6
are set to allow “M” calls.
In order to get the same results as package ‘farms_1.3.1’, you need to set
alpha1=0.5
and alpha2=0.5
.
For exon/genome arrays it is necessary to supply option
and exonlevel
.
Following option
s are valid for exon arrays only:
transcript : | expression levels are computed for transcript clusters, i.e. probe sets containing the same ‘transcript_cluster_id’. |
exon : | expression levels are computed for exon clusters, i.e. probe sets containing the same ‘exon_id’, where each exon cluster consists of one or more probeset s. |
probeset : | expression levels are computed for individual probe sets, i.e. for each ‘probeset_id’. |
Following exonlevel
annotations are valid for exon arrays:
core : | probesets supported by RefSeq and full-length GenBank transcripts. | |
metacore : | core meta-probesets. | |
extended : | probesets with other cDNA support. | |
metaextended : | extended meta-probesets. | |
full : | probesets supported by gene predictions only. | |
metafull : | full meta-probesets. | |
ambiguous : | ambiguous probesets only. | |
affx : | standard AFFX controls. | |
all : | combination of above. |
Following exonlevel
annotations are valid for whole genome arrays:
core : | probesets with category ‘unique’ and ‘mixed’. | |
metacore : | probesets with category ‘unique’ only. | |
affx : | standard AFFX controls. | |
all : | combination of above. |
Exon levels can also be combined, with following combinations being most useful:
exonlevel="metacore+affy" : | core meta-probesets plus AFFX controls |
exonlevel="core+extended" : | probesets with cDNA support |
exonlevel="core+extended+full" : | supported plus predicted probesets |
Exon level annotations are described in the Affymetrix whitepaper ‘exon_probeset_trans_clust_whitepaper.pdf’.
In order to use an alternative SchemeTreeSet
set the corresponding
SchemeTreeSet xps.scheme
.
xpsINICall
is the DataTreeSet
method called by function ini.call
,
containing the same parameters.
Since I/NI-calls distinguish only between informative and non-informative genes, the calls are identical for all samples.
Christian Stratowa
Talloen, W., Clevert D.-A., Hochreiter, S., Amaratunga, D., Bijnens, J., Kass, S., and Gohlmann, H.W.H. (2006), I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data. Bioinformatics 23(21):2897-2902
## first, load ROOT scheme file and ROOT data file scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/")) data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/")) ## I/NI call call.ini <- ini.call(data.test3,"tmp_Test3INI",verbose=FALSE) ## get data.frames snr.ini <- pvalData(call.ini) inf.ini <- presCall(call.ini) head(snr.ini) head(inf.ini) ## plot results if (interactive()) { callplot(call.ini) } rm(scheme.test3, data.test3) gc()