Displaying 7 results from an estimated 7 matches for "assaydata".
2012 Jun 28
1
Merging listed dataset into one
Hello,
I'm wondering how I can merge two featuresets into one.
My dataset is two sets of microarray data and it looks like followings:
> rawData
$v1
TilingFeatureSet (storageMode: lockedEnvironment)
assayData: 2197815 features, 59 samples
element names: channel1, channel2
protocolData
rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ...
LT003990RU_D1_2010-11-04 (59 total)
varLabels: filenamesChannel1 filenamesChannel2 dates1 dates2
varMetadata: labelDescription channel
phenoData...
2007 Sep 25
1
'load' does not properly add 'show' methods for classes extending 'list'
...the Bioconductor package GSEABase
extends 'list'
> library(GSEABase)
> showClass("GeneSetCollection")
Slots:
Name: .Data
Class: list
Extends:
Class "list", from data part
Class "vector", by class "list", distance 2
Class "AssayData", by class "list", distance 2
If I create an instance of this class and serialize it
> x <- GeneSetCollection(GeneSet("X"))
> x
GeneSetCollection
names: NA (1 total)
> save(x, file="/tmp/x.rda")
and then start a new R session and load the data obj...
2020 Sep 24
1
How to use `[` without evaluating the arguments.
...ngTable)[eval(columnQuery), ]
} else {
colDataSubset <- colData(longTable)
}
rowKeys <- rowDataSubset$rowKey
colKeys <- colDataSubset$colKey
if (missing(assays)) { assays <- assayNames(longTable) }
keepAssays <- assayNames(longTable) %in% assays
assayData <- lapply(assays(longTable)[keepAssays],
FUN=.filterLongDataTable,
indexList=list(rowKeys, colKeys))
return(LongTable(colData=colDataSubset, colIDs=longTable at .intern$colIDs ,
rowData=rowDataSubset, rowIDs=longTable at .intern...
2007 Dec 20
1
custom subset method / handling columns selection as logic in '...' parameter
...male Control 0.77
W Male Control 0.27
X Male Control 0.98
Y Female Case 0.94
Z Female Case 0.32
# now the sample use
> (subset1 =subset(expressionSet,sex="Male",type="Control"))
7 columns selected (C F J R U W X)
ExpressionSet (storageMode: lockedEnvironment)
assayData: 500 features, 7 samples
element names: exprs, se.exprs
phenoData
sampleNames: C, F, ..., X (7 total)
varLabels and varMetadata description:
sex: Female/Male
type: Case/Control
score: Testing Score
featureData
featureNames: AFFX-MurIL2_at, AFFX-MurIL10_at, ..., 31739_at (500 t...
2012 Nov 26
1
A problem subsetting a data frame
...: list()
> .. .. ..@ preprocessing : list()
> .. .. ..@ other : list()
> .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
> .. .. .. .. ..@ .Data:List of 1
> .. .. .. .. .. ..$ : int [1:3] 1 0 0
> ..@ assayData :<environment: 0x1078636e8>
> ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
> .. .. ..@ varMetadata :'data.frame': 21 obs. of 1 variable:
> .. .. .. ..$ labelDescription: chr [1:21] " Patien...
2010 Nov 12
0
drosophila2cdf in simpleaffy / affyQCReport
...hM AFFX-Dros-GAPDH_3_at AFFX-Dros-GAPDH_M_at
this I copied as drosophila2cdf.qcdef to the cirectory:
../R/x86_64-pc-linux-gnu-library/2.12/simpleaffy/extdata/drosgenome2cdf.qcdef
I than try to run the analysis again:
> data <- ReadAffy()
> data
AffyBatch (storageMode: lockedEnvironment)
assayData: NA features, NA samples
element names: exprs
protocolData
sampleNames: 10_w1h_021110.CEL 11_wbh_021110.CEL ... 9_dch_021110.CEL
(12 total)
varLabels: ScanDate
varMetadata: labelDescription
phenoData
sampleNames: 10_w1h_021110.CEL 11_wbh_021110.CEL ... 9_dch_021110.CEL
(12 total)...
2008 Apr 14
3
Doing the right amount of copy for large data frames.
Hi there,
Problem ::
When one tries to change one or some of the columns of a data.frame, R makes
a copy of the whole data.frame using the '*tmp*' mechanism (this does not
happen for components of a list, tracemem( ) on R-2.6.2 says so).
Suggested solution ::
Store the columns of the data.frame as a list inside of an environment slot
of an S4 class, and define the '[',