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, ...)DataTreeSet.version="1.3.1" and to 8.0
for version="1.3.0".version="1.3.1" and to 2.0
for version="1.3.0".version="1.3.1" and
version="1.3.0" are implemented. Default is version="1.3.1".SchemeTreeSet.TRUE call data will be added to slots data and detcall.TRUE print status information.DataTreeSet.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="">
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 options 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 probesets. |
probeset: |
| expression levels are computed for individual probe sets, i.e. for each 'probeset_id'. |
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. |
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. |
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.
farms, mas5.call## 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()
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