Displaying 5 results from an estimated 5 matches for "readtargets".
2007 Nov 13
0
need help with error message:Error in lm.fit(design, t(M)) : incompatible dimensions
...[1:22690, 1:2] 12.0 11.3 13.0 11.6 10.3 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:22690] "1415670_at" "1415671_at" "1415672_at" "1415673_at"
...
..$ : chr [1:2] "A1_xen1_1_1.CEL" "A2_xen2a_5_2.CEL"
targets<-readTargets("xen1shrt.txt") # Read target files
>targets
Name FileName Target
1 A1_xen1_1_1 A1_xen1_1_1.CEL A_xen
2 A2_xen2a_5_2 A2_xen2a_5_2.CEL A_xen
3 A3_xen2b_6_3 A3_xen2b_6_3.CEL A_xen
4 B1_cr1_2_4 B1_cr1_2_4.CEL B_crp
5 B2_cr2a_9_5 B2_cr2a_9_5.CEL B_crp
6 B3...
2009 Mar 13
0
Singal channel spike in controls with custom microRNA slides - Normalization help needed
...per array or the mean of all the controls per array.
The gal file is also loaded with all the array structure. Each block
contains spike in controls.
Here is the code:
library(limma)
library(RColorBrewer)
library(vsn)
Cy5 <- "F635 Mean"
Cy5b <- "B635 Mean"
targets <- readTargets("targets.txt")
#My gpr files do only contain 1 channel (Cy5)
RG <- read.maimages(
targets$FileName,source="genepix",columns=list(R=Cy5,G=Cy5, Rb=Cy5b,
Gb=Cy5b))
RG$G <- NULL
RG$Gb <- NULL
RG$genes <- readGAL("array_human_mirs.gal")
#Here are my spike in co...
2009 May 06
1
[Fwd: loading SPOT file]
-------------- next part --------------
An embedded message was scrubbed...
From: Barbara Cegielska <barceg at ibch.poznan.pl>
Subject: loading SPOT file
Date: Wed, 06 May 2009 16:48:35 +0200
Size: 1151
URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20090506/e35e3f7e/attachment-0002.eml>
2009 Feb 12
0
Error Message: Error in dim(data) <- dim : attempt to set an attribute on NULL
...f an object.
dim(adf)
#rowNames columnNames
# 28 2
rownames(adf)
#NULL
#read in galfile
readGAL("Galfile.gal")
#Create eset object
eSet<-new("ExpressionSet",exprs=myexprdata,phenoData=adf,annotation="Galfile.gal")
#Read in targets file
targets <- readTargets("targets.txt")
targets
# Set up character list defining your arrays, include replicates
TS <- paste(targets$Species, targets$Time, sep=".")
#This script returns the following:
TS
# Turn TS into a factor variable which facilitates fitting
TS <- factor(TS)
#This script retur...
2007 Jul 30
0
problems in limma
...ing. Will the above-mentioned warnings
affect the reliability of the final result? Can I continue to the next
step?
Thanks!
Dejian Zhao
++++++++++++++++++ Program Starts +++++++++++++++++++++
> library(limma)
> library(statmod) #duplicateCorrelation requires this package.
> targets<-readTargets()
> targets
Cy3 Cy5 FileName Date
1 PLAIN PLATEAU Locust 186.gpr 2006-5-31
2 PLAIN PLATEAU Locust 187.gpr 2006-5-31
3 PLAIN PLATEAU Locust 188.gpr 2006-5-31
4 PLAIN PLATEAU Locust 189.gpr 2006-5-31
5 PLAIN PLATEAU Locust 190.gpr 2006-5-31
6 PLAIN PLATEAU L...