Displaying 20 results from an estimated 10000 matches similar to: "(no subject)"
2010 Nov 12
0
drosophila2cdf in simpleaffy / affyQCReport
Hi everybody,
I have a problem when trying to do the quality control with the packages
simpleaffy and affyQCReport with the drosophila chip 2.0
At first I got the messeage, that the *.qcdef file is not there. I followed
the instructions in tha manual and created the file like that:
array drosophila2cdf
alpha1 0.05
alpha2 0.065
spk bioB AFFX-r2-Ec-bioB-3_at
spk bioC AFFX-r2-Ec-bioC-3_at
spk bioD
2003 Sep 11
1
discrepancy between R and Splus lm.influence() functions for family=Gamma(link=identity)
Hello,
I am looking for an explanation and/or fix for a discrepancy in the behaviour of the R lm.influence() function [ version R 1.5.0 (2002-04-29) ] and the same function in Splus [ Splus version 5.1 release 1, running on SGI IRIX 6.2]. The discrepancy is of concern because I am migrating some Splus scripts to R and need to ensure consistency of results.
Specifically, when I fit a glm()
2006 Jan 30
0
Anova help
Hello all,
I am trying to perform ANOVA on my sample data given below to see if any
gene(column 1 stands for gene names) is differentially expressed after
subjecting it to the 6 different experiments(columns 2 to 7 are
experiments).
Gene
14A_U133A_Detection
14B_U133A_Signal
88A_U133A_Signal
88B_U133A_Signal
183A_U133A_Signal
183B_U133A_Signal
AFFX-BioB-5_at
403
409.3
611.5
2005 Dec 01
1
Transfer String Array from R to java
I have a data frame which has the following data.
data<-read.table("table.txt",header=TRUE)
data
X14A_U133A_StatPairs X14A_U133A_Detection X14B_U133A_Signal
1 AFFX-BioB-5_at 403.0 409.3
2 AFFX-BioB-M_at 757.3 574.4
3 AFFX-BioB-3_at 284.4 327.3
4 AFFX-BioC-5_at
2012 Oct 07
1
BioConductor package: 'oligo'
Dear Help,
After loading the pd.Citrus library and checking the DataFrame, I ran
> the R code for:
>
> 1) 'oligo'
>
>
>
> {> library(pd.citrus)
> Loading required package: RSQLite
> Loading required package: DBI
> > data(pmSequence)
>
> > show(pmSequence)
> DataFrame with 341730 rows and 2 columns
> fid sequence
> <integer>
2005 Aug 31
1
Bioconductor and R-devel
Hi,
I have built R (current development version) and BioConductor 1.7
with portland group compiler on a AMD Opteron.
When I ran qc assessment on Affymetrix latin square data set, I got the
following output,
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
2005 Nov 25
1
read.table without sep
Hello all,
I have a data file table.txt which i have attached. I am trying to pass the
columns as arguments to a function "totnorm" where i am displaying a total
normalization plot. The function is given below:
totnorm<-function(x,y){scale<-sum(x)/sum(y);xlab<-colnames(x);ylab<-colnames(y);x1<-x[[1]];y1<-scale*y[[1]];plot(x1,y1,xlab=xlab,ylab=ylab,col=6,
col.lab=4);}
2005 Nov 25
1
read.table without sep
Hello all,
I have a data file table.txt which i have attached. I am trying to pass the
columns as arguments to a function "totnorm" where i am displaying a total
normalization plot. The function is given below:
totnorm<-function(x,y){scale<-sum(x)/sum(y);xlab<-colnames(x);ylab<-colnames(y);x1<-x[[1]];y1<-scale*y[[1]];plot(x1,y1,xlab=xlab,ylab=ylab,col=6,
col.lab=4);}
2004 Jan 22
1
Calculation of normalised red and green intensities
Dear Sir/Madam,
I could succesfully normalise my microarray data using marrayNorm package.
However, i have not been able to get normalised red and green channel
intensities through R package. Is there a possibility to write a formula
to calculate back the red and green channel intensities after normalisation
of the data. Do I need to incorporate this formula in my R script? I am
biologist
2003 Dec 04
2
RE: R performance questions
Hi--
While I agree that we cannot agree on the ideal algorithms, we should be
taking practical steps to implement microarrays in the clinic. I think
we can all agree that our algorithms have some degree of efficacy over
and above conventional diagnostic techniques. If patients are dying
from lack of diagnostic accuracy, I think we have to work hard to use
this technology to help them, if we
2011 Oct 26
3
FOR loop with statistical analysis for microarray data
hi all
i started recently using R and i found myself stuck when i try to
analyze microarray data.
i use the "affy" package to obtain the intensities of the probes, i
have two CTRs and two treated.
HG.U133A.Experiment1.CEL HG.U133A.Experiment2.CEL
HG.U133A_Control1.CEL HG.U133A_Control2.CEL
1007_s_at 2156.23115 467.75615
364.60615 362.11865
2011 Feb 17
0
[BioC] Make.cdf.package error
Hi everybody,
I tried to analyze a custom Affymetrix 3'-biased Array. So I wanted to make
a cdf package. (My CDF file size is 1.12Go).
I tried several methods but the same error occured
Method 1
> #Set the working directory
> setwd("D:/Analyse R/Cel files")
> #library to create cdf env
> library("makecdfenv")
>#Create cdf environment
>pkgpath
2004 Oct 04
2
Help with Affymetrix data
I have CEL files from Affymetrix Mouse Array 430_2 and am trying to get the
the individual PM intensities (11 per gene) for each sample. I would like to
write out this into a tab delimited text file. Where am I stalling? This is
what I've done:
Change dir(to where CEL files are saved)
Data <- ReadAffy()
eset <- rma(Data)
write.exprs(eset, file="mydata.txt")
With this I am
2003 Oct 30
0
Release of Bioconductor 1.3
The Bioconductor core group would like to announce the 1.3 release of
the Bioconductor software. There are many new packages as well as
several major upgrades and fixes in older packages, and users are
encouraged to check them out. Release 1.3 is intended to be operated
with R version 1.8.X, which can be obtained at CRAN
(http://cran.r-project.org/)
-- WHAT FEATURES DOES THIS RELEASE PROVIDE?
2003 Oct 30
0
Release of Bioconductor 1.3
The Bioconductor core group would like to announce the 1.3 release of
the Bioconductor software. There are many new packages as well as
several major upgrades and fixes in older packages, and users are
encouraged to check them out. Release 1.3 is intended to be operated
with R version 1.8.X, which can be obtained at CRAN
(http://cran.r-project.org/)
-- WHAT FEATURES DOES THIS RELEASE PROVIDE?
2012 Apr 25
0
FW: [BioC] Overlay Gene Expression on SNP (copy number) data
Dear All,
Thank you kindly for such detailed replies. I was looking to overlay data using algorithms so that i am able to tell which genes are differentially expressed due to changes in copy number. I did a pubmed search and found only 7 literature pieces all of which use in-house algorithms. I am yet to explore Gviz since it wouldn't work on R 2.14, would try it after upgrading to R 2.15.
2005 Oct 31
1
write.table call
Hi,
I use write.table() to write a file to an external xls file. the column names left-shift one position in output file. I check with col.names() row.names(), the file is fine. How to prevent the shifting?
I71 I111 I304 I307 I305 I306 I114 I72
AFFX-BioB-5_at 6.66435 6.787807 5.335962 5.250163 6.47423 5.882104 5.965109 6.591687195
AFFX-BioB-M_at 6.163227 5.965427 4.665569 2.743531 6.097244
2007 Aug 03
4
FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
Hi all,
What are current methods people use in R to identify
mis-spelled column names when selecting columns
from a data frame?
Alice Johnson recently tackled this issue
(see [BioC] posting below).
Due to a mis-spelled column name ("FileName"
instead of "Filename") which produced no warning,
Alice spent a fair amount of time tracking down
this bug. With my fumbling fingers
2009 Jul 03
2
normalised curve fitting with error bars
Dear List,
My data consist of nine columns and about 50,000 rows. It looks like
this.
-9.0225 3.46464 2.80926 -0.3847 3.73735 1.1058 -2.98936 1.38901 -8.1846
-2.4315 -5.1189 1.8225 3.3798 1.7874 4.693 -3.9286 1.4266 5.7849
-3.4894 -4.0305 3.7879 3.5195 2.9186 2.8685 -6.126 4.978 4.9381
4.5282 3.62558 -3.0455 4.6518 1.39746 0.68652 3.5708 -3.6404 -4.2963
-1.3183 0.6752 -4.0382 -2.5386
2003 Aug 13
4
big data file geting truncated
I am very new to R. I was trying to load some publicly available Expression
data in to R.
I used the following commands
mydata<-read.table("dataALLAMLtrain.txt", header=TRUE, sep
="\t",row.names=NULL)
It reads data without any error
Now if I use
edit(mydata)
It shows only 3916 entries, whereas the actual file contains 7129 entries)
My data is something like
Gene Description