User: viritha kaza
viritha kaza • 580
- Reputation:
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Posts by viritha kaza
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0
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... Hi James,
I used row.names =1 as suggested by you and Martin.I did not get any
error
and included these steps.
>fit_pair <- eBayes(fit_pair)
> topTable(fit_pair, coef="TreatT")
and got a list
ID logFC AveExpr t
P.Value adj.P.Val B
1 ...
written 6.5 years ago by
viritha kaza • 580
0
votes
2
answers
2.1k
views
2
answers
... Hi group,
I am trying to perform paired t-test for 6 samples which are paired
one is
from normal tissue of the subject and the other is tumor tissue of the
same
subject.
I am following the code as mentioned in the Limma User guide,p.40,8.3
Paired Samples)
Code:
>source("http://bioconductor.org/b ...
written 6.5 years ago by
viritha kaza • 580
• updated 6.5 years ago by
James W. MacDonald ♦ 46k
0
votes
0
answers
520
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... Hi group,
I have to design the paired ttest for multiple subgroups for 80
patients
with tumor and their respective normal samples. I am new to using
multiple
groups and I have normally used just tumor versus control.
Subgroups:
Group(160)- Tumor(80), Normal(80)
Gender(80)- Female(27), Ma ...
written 6.5 years ago by
viritha kaza • 580
0
votes
0
answers
318
views
0
answers
... Hi Group,
When I am runing GAIA I am getting an empty result file with just the
column names.
Previously I ran GAIA using the gist.RData and gist_markers.RData and
I did
get the result for this.
The only difference between my file and gist file was that I dont have
chromosome 14 data in my file.Do y ...
written 6.6 years ago by
viritha kaza • 580
0
votes
1
answer
473
views
1
answer
... Hi John,
I had asked you of some questions regarding cghMCR.
Before my data use to give a SGOL plot.
I am not sure if there is any little change that I am doing.
Code:
>source("http://bioconductor.org/biocLite.R")
>biocLite(c("CNTools","cghMCR"))
> library(CNTools)
>require(CNTools, quie ...
written 6.7 years ago by
viritha kaza • 580
• updated 3.1 years ago by
pascal.gellert • 0
0
votes
0
answers
553
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... Hi John,
Thanks for your reply.
I saw http://rss.acs.unt.edu/Rdoc/library/cghMCR/html/cghMCR.html
here that
*Usage*:
cghMCR(segments, gapAllowed = 500, alteredLow = 0.03, alteredHigh =
0.97, spanLimit = 2e+07, recurrence = 75)
*Arguments*
segments
:segments is a data frame extracted from th ...
written 6.8 years ago by
viritha kaza • 580
0
votes
1
answer
556
views
1
answer
... Dear Group,
I saw this question asked but did not find a reply and I have the same
question.
I was looking for a package that provides functions to identify
minimum
common genomic regions of interests based on segmented copy number
data from
multiple samples. I've found cghMCR package could be very ...
written 6.8 years ago by
viritha kaza • 580
• updated 6.8 years ago by
Jianhua Zhang • 20
0
votes
0
answers
279
views
0
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... Hi group,
I am trying to right a code to do the following
This is how the test file looks like:
Chr
start
end
sample1
sample2
chr2
9896633
9896683
0
0
chr2
9896630
9896690
0
0
chr2
14314039
14314098
0
-0.35
chr2
14404467
14404502
0
-0.35
chr2
14421718
14421777
-0.43
- ...
written 6.8 years ago by
viritha kaza • 580
0
votes
1
answers
2.8k
views
1
answers
Comment:
C: median normalization
... Hi James,
Thanks for your quick reply.
So my last step should be
exprs<-eset-median+median1.
Is it?
In the paper they say
"RNA fluorescent labeling reaction and hybridization were performed
using
the Affymetrix Gene Chips HG-U133A and HG-U133B according to the
manufacturers instructions (http ...
written 6.9 years ago by
viritha kaza • 580
0
votes
1
answer
2.8k
views
1
answer
... Hi group,
I am trying to replicate a dataset GSE4824 from a paper.
There are actually 3 platforms in them. But right now I am
concentrating
only on one platform GPL570.This contains 6 arrays.
I have written the code to perform Microarray Suite version 5.0 (MAS
5.0)
using Affymetrix default analysis ...
written 6.9 years ago by
viritha kaza • 580
• updated 6.9 years ago by
James W. MacDonald ♦ 46k
Latest awards to viritha kaza
Popular Question
6.5 years ago,
created a question with more than 1,000 views.
For using limma package for paired t-test: Error: (subscript) logical subscript too long
Popular Question
6.5 years ago,
created a question with more than 1,000 views.
For median normalization
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