Displaying 11 results from an estimated 11 matches for "cy3".
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2003 Sep 16
3
Question in Using sink function
...the following writes nothing into
"all.Rout"
file? If the "for" loop is removed, t.test output can be written into
"all.out".
Thanks in advance.
Minghua Yao
......
zz <- file("all.Rout", open="wt")
sink(zz)
for(i in 1:n)
{
Cy3<-X[,2*i-1];
Cy5<-X[,2*i];
t.test(Cy3, Cy5)
}
sink()
close(zz)
......
2008 Feb 14
1
How to check cy5 and cy3 values were lowess normalized
Hi,
I have some microarray data, cy5 and cy3 values are in log2. Is there a
way to check they have undergone lowess normalization ?
Thanks
Stanley
[[alternative HTML version deleted]]
2009 Feb 09
1
XML package- accessing nodes based on attributes
...Name="PatientReference" eValue="TCGA-06-0875-01A"/>
<Characteristic Type ="Patient" eName="SampleType" eValue="TUMOR"/>
<Characteristic Type ="Patient" eName="SampleMarker" eValue="cy3"/>
<Characteristic Type ="Patient" eName="PatientDateOfBirth" eValue="080808"/>
<Characteristic Type ="Patient" eName="PatientGender" eValue="M"/>
<Characteristic Type...
2004 Dec 13
0
about vsn
Hello sir:
As to the "variance stabilization" method which is applied in the "vsn"package under R environment,here's a question about the ratio of the 2 channels:
After applying vsn,we can get new_cy5 and new_cy3 intensity according to the original cy5 and cy3 intensity respectively. And the new_cy5 new_cy3 are similar with ln(intensity).
But how can I calculate the ratio=cy5/cy3 ?
If the new_cy5 and new_cy3 is log2(intensity),the ratio equals to 2^(log2cy5-log2cy3),but as to vsn,how to get the ratio?
Si...
2009 May 06
1
'RG' looks like a pre-2.4.0 S4 object: please recreate it
...sage:
'RG' looks like a pre-2.4.0 S4 object: please recreate it
> objects()
[1] "RG"
> names(RG)
[1] "R" "G" "Rb" "Gb" "printer" "genes" "targets"
> RG$targets
FileName Cy3 Cy5
c1 a1koc1.spot Pool C57BL/6
c2 a1koc2.spot Pool C57BL/6
c3 a1koc3.spot Pool C57BL/6
c4 a1koc4.spot Pool C57BL/6
c5 a1koc5.spot Pool C57BL/6
c6 a1koc6.spot Pool C57BL/6
c7 a1koc7.spot Pool C57BL/6
c8 a1koc8.spot Pool C57BL/6
k1 a1kok1.spot Pool ApoAI-/-
k2 a1kok2.spot Pool ApoAI-/-...
2007 Dec 06
1
finding most highly transcribed genes - ranking, sorting and subsets?
...interested in finding out which genes are the most highly up-
or down-regulated (which I have done using the linear models and Bayesian
statistics in Limma), but I also want to know which genes are consistently
highly transcribed (ie. they have a high intensity in the channel of
interest eg. Cy5 or Cy3 across the set of experiments). I might have missed
a straight forward way to do this, or a valuable function, but I've been
using my own methods and going around in circles.
So far I've normalized within and between arrays, then returned the RG
values using RG<-RG.MA, then I ranked...
2007 Mar 02
0
LIMMA contrast.matrix
...National Center for Cool & Cold Water Aquaculture
11861 Leetown Road
Kearneysville, WV 25430
Voice: (304) 724-8340 Ext. 2141
Email: roger.vallejo@ars.usda.gov <mailto:roger.vallejo@ars.usda.gov>
****************************************
> targets
SlideNumber FileName Cy3 Cy5
ml12med 12 ml12med.spot CD4 CD8
ml13med 13 ml13med.spot CD8 CD4
ml14med 14 ml14med.spot DN CD8
ml15med 15 ml15med.spot CD8 DN
ml16med 16 ml16med.spot CD4 DN
ml17med 17 ml17med.spot DN CD4
> design <- modelMatrix(targets, ref="CD4")
Found unique target names:
CD4 CD8...
2004 Nov 12
0
Design Matrix
Dear all,
I need some help on matrix design and B statistics by using limma package.
I want to compare gene expression in 2 groups of cDNA samples.
The experiment compares 4 treated mice(#1,#2,#3,#4) and 4 control mice
(#5,#6,#7,#8).
The target file is
FileName Cy3 Cy5
mice1.spot Control_#5 Treat_#1
mice2.spot Treat_#1 Control_#5
mice3.spot Control_#6 Treat_#2
mice4.spot Treat_#3 Control_#7
mice5.spot Control_#8 Treat_#4
The first slide (mice1.spot) and the second slide(mice2.spot) are
dye-swap. There is no common reference....
2007 Apr 20
2
limmaGUI
Dear all,
I have a question about limmaGUI that is usually run in R environment.
My problem is loading data into the programm. I have 6 gpr files that
apparently are not compatible with limma. Everytime I'm trying to load
the data (including a RNA targets file, an error appears:Error reading
files. that I'm not sure,but seems to have something to do with the
format of my files
2007 Jul 30
0
problems in limma
...ings
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 Locust 191.gpr 2006-5-31
7...
2008 Jun 30
4
Rebuild of kernel 2.6.9-67.0.20.EL failure
Hello list.
I'm trying to rebuild the 2.6.9.67.0.20.EL kernel, but it fails even without
modifications.
How did I try it?
Created a (non-root) build environment (not a mock )
Installed the kernel.scr.rpm and did a
rpmbuild -ba --target=`uname -m` kernel-2.6.spec 2> prep-err.log | tee
prep-out.log
The build failed at the end:
Processing files: kernel-xenU-devel-2.6.9-67.0.20.EL
Checking