User: julin@aecom.yu.edu
julin@aecom.yu.edu • 80
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Posts by julin@aecom.yu.edu
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... Dear List,
I am using limma to analyze a affy ST1.0 dataset.
I have 6 patients from which I have two tissue types: tumor and non-
tumor.
One of the sample has a technical repeat, resulting 12 arrays.
I would like to compare tumor vs. non-tumor and incorporate the
pairing and
technical repeat ...
written 9.0 years ago by
julin@aecom.yu.edu • 80
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... Hi dear all
I am using the heatmap.2 function in the gplots package to draw a
heatmap of
297 gene list. The plot looks very nice. But since the rows(genes)
were
reordered along with the dendrogram, is there any way to output this
reordered gene list from heatmap.2()?
The code I used is as below ...
written 9.7 years ago by
julin@aecom.yu.edu • 80
• updated
9.7 years ago by
Di Wu • 190
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... Dear All,
1. I am working on a microarray dataset. The array platform is
GeneChip Mouse Gene 1.0 ST Array. The experiment design is very
straight
forward: two groups comparison--control vs. treatment, with three
chips in
each group.
2.
3. Below is my code:
> library(limma)
> T ...
written 9.7 years ago by
julin@aecom.yu.edu • 80
• updated
9.7 years ago by
James W. MacDonald ♦ 51k
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...
Dear List,
I am working with six 27K human cDNA chips.Three of them are for
Average
Primary Tumor Cells and another three are for Invasive cells.In all
chips,
the reference in on the red channel, and the tumor samples are on the
green channel. Here is my target file:
ID FileName Cy3 ...
written 10.6 years ago by
julin@aecom.yu.edu • 80
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... Dear list,
I am writing to ask if anyone can help me to define a design matrix
for
our experiment.
I am working with MoGene ST1.0 chips.Samples are from WT or HIV-
transgenic
mouse bone marrow-derived macrophages that we grew in dishes and then
either exposed to TB or not for 24 hours. Each pair i ...
written 11.0 years ago by
julin@aecom.yu.edu • 80
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Comment:
C: problem with function rma
... Martin,
It works after I change the order of phenoData names! And I will
update both
R and bioconductor today.
Thanks a lot for your help!
Juan
-----Original Message-----
From: Martin Morgan [mailto:mtmorgan@fhcrc.org]
Sent: Tuesday, May 29, 2007 9:27 PM
To: Juan Lin
Cc: bioconductor at stat.mat ...
written 12.3 years ago by
julin@aecom.yu.edu • 80
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...
Hello Bioconductorers,
I am working with 12 affy rat2302 chips recently. It was OK when I
tried to
read my cel files into R:
> RatData<-ReadAffy()
> list.celfiles()
[1] "Rat 16hrs-1-2113.CEL" "Rat 16hrs-2-2114.CEL" "Rat
16hrs-3-2115.CEL"
[4] "Rat 30hrs-1-2116.CEL" "Rat 30hrs-2-2117. ...
written 12.3 years ago by
julin@aecom.yu.edu • 80
• updated
12.3 years ago by
Seth Falcon • 7.4k
0
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2
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... Dear All:
Recently I did some Ambion bioarray (one color hybridization), and got
data of 6 arrays in 3 gpr files(in each gpr file there will be two
array
which being designated as block1 and block 2)from GenePix. I am having
trouble to normalize my data. Can anyone kindly give me any clue?
Thanks a ...
written 12.8 years ago by
julin@aecom.yu.edu • 80
• updated
12.8 years ago by
Al Ivens • 270
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