User: viritha kaza

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viritha kaza580
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Posts by viritha kaza

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Comment: C: using limma package for paired t-test: Error: (subscript) logical subscript too
... 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 5.8 years ago by viritha kaza580
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using limma package for paired t-test: Error: (subscript) logical subscript too long
... 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 ...
limma written 5.8 years ago by viritha kaza580 • updated 5.8 years ago by James W. MacDonald45k
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Limma design for paired t-test for multiple subgroups
... 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 5.9 years ago by viritha kaza580
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using GAIA
... 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 ...
gaia written 6.0 years ago by viritha kaza580
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SGOL plot
... 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 ...
cghmcr written 6.1 years ago by viritha kaza580 • updated 2.4 years ago by pascal.gellert0
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cghMCR package:Is it possible to find MCR by not usingDNAcopy object?
... 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 ...
process dnacopy cghmcr written 6.1 years ago by viritha kaza580
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cghMCR package:Is it possible to find MCR by not using DNAcopy object?
... 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 ...
dnacopy cghmcr written 6.1 years ago by viritha kaza580 • updated 6.1 years ago by Jianhua Zhang20
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R functions
... 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 6.2 years ago by viritha kaza580
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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 manufacturer’s instructions (http ...
written 6.2 years ago by viritha kaza580
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median normalization
... 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 ...
microarray normalization written 6.2 years ago by viritha kaza580 • updated 6.2 years ago by James W. MacDonald45k

Latest awards to viritha kaza

Popular Question 5.8 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 5.8 years ago, created a question with more than 1,000 views. For median normalization

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