Displaying 17 results from an estimated 17 matches for "samplename".
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samplenames
2011 Mar 31
1
Assign Names of columns in data.frame dinamically
...aste(Dir),'.txt$');
ecg = data.frame(ncol=1);
len = length(txtfiles);
for (i in 1:5 ) {
# i <- 1;
filename = paste(projectDir, "/" ,
txtfiles[i],sep='');
sample = read.table(filename, nrow=75000);
sampleName = filename; sampleName=gsub("./",
"",sampleName); sampleName=gsub(".txt", "", sampleName);
temp <- sample$V2;
names(temp) <- sampleName;
ecg = cbind(ecg, temp);
# }
Thanks and sorry for my english.
--...
2005 May 29
2
"text"-function: adding text in an x,y-plot
Hello R-friends,
i have a question to the "text"-function.
a little test-dataset for better understanding:
-the dataset was imported with read.table(....,header=TRUE)
s1-s10 are the samplenames
var1 var2 var3
s1 1 1 2
s2 2 3 1
s3 2 2 3
s4 5 4 3
s5 4 2 3
s6 6 3 2
s7 8 5 4
s8 7 2 1
s9 9 3 2
s10 8 6 4
-then i??ve performed a pincipal component analysis with prcomp
-for displaying the r...
2010 Oct 05
2
Plotting x-axis labels perpendicular to the axis
Hi,
The following command: axis(1, at= 1:50, labels= sampleNames(data)) produces
an X-axis with 50 ticks and labels drawn from the sampleNames namespace.
Problem is the labels at each tick are printed parallel to the x-axis and
thus run into each other. How do I specify for the labels to be printed
perpendicular to the x-axis?
Thanks in advance.
Anjan
--
====...
2007 Jun 20
0
shoudl I use apply, sapply, etc instead of a "for loop"?
...e.001', 'income.002')
sapply(filenames,function(x) { save( list=x , file = paste(x ,'.r', sep ='') ) })
rm(sat.001,sat.002,income.001,income.002,filenames)
ls() #
##############
#my for loop
divide = function(x,y) {x/y}
#creates a custom function
#inputs to my loop:
samplenames=c('001','002')
x.name='sat'
y.name='income'
fun='divide'
for (i in 1:length(samplenames) ) {
x.name.suf = paste(x.name,samplenames[i],sep='.')
#name of x file on hrd drive
y.name.suf = paste(y.name,samplenames[i],sep='.')
#name of y file...
2010 May 27
2
Methods to explore R data structures
...ss() to see what the object is. str() /
attributes() to probe inside the object, and something@something$something
to walk it and explore. Is there any other way? Also, without reading
documentations, is there a way to know what functions are available to
extract data from it? For example, there is sampleNames() which works on
ExpressionSet and AnnotatedDataFrame (which is a part of ExpressionSet). How
do I know they are available (as sometimes I can't recall where I've seen
them and I forgot the function names). And what are R functions? Are those
two separate functions or polymorphic functions...
2011 Oct 07
1
Creating One Single Object with Phenotype and Expression Data
...<-
paste(processedDir,"/",strInputAccession,"_default_exprs.csv",sep="")
if(file.exists(sampleFile)){
affyobj <- try(ReadAffy(filenames=read.table(sampleFile,as.is
=T,header=FALSE)[,1]))
if(class(affyobj)=="try-error"){
rm(affyobj)
}else{
sampleNames(affyobj) <- sub("\\..*","",sampleNames(affyobj)) #get rid
of .CEL etc extension, just keep GSM
}
}
if(!exists("affyobj")){
mdExprs <- as.matrix(read.csv(defaultExprs,row.names=1))
if( min( mdExprs, na.rm = TRUE ) >= 0 & max( mdExprs, na.rm = TRUE...
2010 Mar 04
6
help
Hi all ,
I have one query.
i have list of some .cel files. in my program i have to mention the path of
these .cel files
part of my program is,
rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*,
sampleNames=sample.names, phenoData=pheno.data,
cdfname=cleancdfname(hg18_Affymetrix U133A)))
in the place of "datadir" i have to mention the character string of the
directory of these .cel files. I don't know how to give the path for all
these files.
i set the path as given below,
> rna...
2005 Nov 16
2
X11 error in png
...png(paste(savepath,"a_rnaplot.png",sep = ""),width = fwidth, height = fheight,pointsize = fpointsize);
data_deg <- AffyRNAdeg(data_cel)
plotAffyRNAdeg(data_deg,col=cols,lty=1,lwd = "2")
#a <- par("fin")
legend("bottomright",sampleNames(data_cel),col=cols,lty=1)
RNAdegSlope = cbind("Sample Names" = data_deg$sample.names, "RNA Deg Slope" = data_deg$slope)
write.csv(RNAdegSlope, file = paste(savepath,"RNAdegSlope.csv",sep = ""))
dev.off()
I got this error message:
Error in X1...
2012 Nov 26
1
A problem subsetting a data frame
..... .. .. ..$ f.u : chr [1:128] "BMT / DEATH IN CR" "REL" "REL" "REL" ...
> .. .. .. ..$ date last seen: chr [1:128] NA "8/28/2000" "10/15/1999" "1/23/1998" ...
> .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns"
> .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
> .. .. .. .. ..@ .Data:List of 1
> .. .. .. .. .. ..$ : int [1:3] 1 1 0
> ..@ featureData :Formal class 'AnnotatedDataFrame' [p...
2012 Aug 05
2
setMethod sometimes fails to set package slot when signature has trailing 'ANY'
...matchSigLength at line 603.
The context for this is the thread starting at
https://stat.ethz.ch/pipermail/bioconductor/2012-August/047241.html
where a complicated package dependency and attempt to redefine an
existing method leads to
Error : package slot missing from signature for generic 'sampleNames<-'
and classes LumiBatch, ANY
cannot use with duplicate class names (the package may need to be
re-installed)
Martin
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-...
2010 Nov 12
0
drosophila2cdf in simpleaffy / affyQCReport
...2cdf.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)
varLabels: sample
varMetadata: labelDescription
featureData: none
expe...
2009 Aug 25
1
package dependencies specification
...blem is in the way
I have specified dependencies in NAMESPACE or DESCRIPTION. It appears that
dependecies need to be specified in both.
These two files are shown below.
------------------------------
NAMESPACE
export(nv.batch.normalize, norm.options, combine.norm.esets,
subset.norm.eset, update.sampleNames)
import(affy, simpleaffy, hgu133acdf, hgu133plus2cdf)
importFrom(affyio, read.celfile, read.celfile.header)
DESCRIPTION
...
Depends: R (>= 2.5.0), Biobase
Imports: affy, affyio, simpleaffy, hgu133acdf, hgu133plus2cdf
--------------------------------
I'd appreciate any help.
Thank you....
2011 Oct 07
0
Creating One Single Object Linking Multiple Datapoints
...prs.csv",sep="")
>>
>> if(file.exists(sampleFile)){
>> affyobj<- try(ReadAffy(filenames=read.**table(sampleFile,as.is
>> =T,header=FALSE)[,1]))
>> if(class(affyobj)=="try-error"**){
>> rm(affyobj)
>> }else{
>> sampleNames(affyobj)<- sub("\\..*","",sampleNames(**affyobj)) #get
>> rid
>> of .CEL etc extension, just keep GSM
>> }
>> }
>>
>> if(!exists("affyobj")){
>> mdExprs<- as.matrix(read.csv(**defaultExprs,row.names=1))
>> i...
2006 Mar 16
2
Bioconductor package on linux machine
...e files and installed in the directory
/usr/lib64/R/library
but when i try using those files, they show as not installed.
Anybody encounter this problem before OR is there something else i am
doing wrong?
Following is the sequence of stpes i used first:
1) library(affy)
2) pcpc <-
ReadAffy(sampleNames=c("107762","110662","110682","110792","110802","111301","111611","111781","111801","154272","160881"))
3) pc <- rma(pcpc)
Error in library("hgu133plus2cdf", lib.loc = NULL...
2007 Dec 20
1
custom subset method / handling columns selection as logic in '...' parameter
...e 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 total)
fvarLabels and fvarMetadata description: none
experimentData: use 'ex...
2006 May 22
8
flickr tag question
hey,
i am using the flickr wrapper for ruby and need to access the tags of a
specific photo. i got all the rest working. i must admit i am kind of new to
ruby, but i tried and tried and couldn''t figure it out. among other things i
want to read geotags like in my example here:
http://www.flickr.com/photos/whoisstan/146634506/
i''m sure it is deadsimple and i just overlooked it.
2009 Sep 19
3
Replacing values in dataframes
Hi,
This is a question of a newbie getting into the exciting world of R.
I have several dataframes in the same format as NAD:
> NAD[1:3,1:3]
Sample.Id Main.abs..1 Main.abs..2
148 10a 0.04836 0.04994
167 11a_1109 0.32245 0.36541
173 11b_1109 0.29293 0.32815
What I want to do is to replace the Sample.Id with a corresponding number.The number