User: Bade

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Bade310
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Posts by Bade

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Compute test-score statistical significance using control-scores from shuffled p
... @Gordon Smyth: Many thanks for replying and link to your paper. I almost lost hope of getting help on this. Here baskets (B1 and B2) represent “w” and “c” strands, both independent of each other as far as this study is concerned. In above example we are just concerned about “w” strand. The “apple” ...
written 20 months ago by Bade310
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Compute test-score statistical significance using control-scores from shuffled population
... Hi List, I couldn't get answer to this in other forums so posting here with hopes of help in computing statistical significance of my data. Suppose I have 2 baskets (B1 and B2) on a table each with mix of apple and oranges, and there are 10 such tables (T1 to T10. Now, I have computed the log-odd s ...
statistics R hypotheses written 20 months ago by Bade310
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Clustering sequence on similarity using percentage identity matrix
... I have a set of 400 nucleotide sequences and want to cluster them on basis of similarity. For clustering, I am expecting a similarity <=45% among members of a cluster. Also, there will be a few sequences that do not show similarity to any other member. Is there any clustering approach that allow ...
alignment clustering written 2.4 years ago by Bade310
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Comment: C: Two-class unpaired test using LIMMA
... @James - I added dummy code so that we can have some variables for the correct answer/code. Sorry, posted my comment as answer. Thanks for helping. Bade ...
written 3.0 years ago by Bade310
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Comment: A: Two-class unpaired test using LIMMA
... Hi James, Sorry I forgot to put in the replicates info. Here is the modified code: AF.mydata <- ReadAffy() AF.esetRMA<-rma(AF.mydata) AF.sampletype <- c('Norm1','Norm1','Norm2','Norm2','Norm3','Norm3' 'Mut1','Mut1','Mut2','Mut2','Mut3',Mut3','Mut4','Mut4') AF.group <-factor(AF.samplet ...
written 3.0 years ago by Bade310 • updated 3.0 years ago by Gordon Smyth32k
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Two-class unpaired test using LIMMA
... Hi All, I want to identify genes that are significantly associated with normally developing tissues. The data sets which I have can be divided into two classes:  1. Normally developing - Samples from wild type tissues  2. Impaired development - Samples from mutants  Both classes have samples fro ...
limma differential expression sam written 3.0 years ago by Bade310 • updated 3.0 years ago by James W. MacDonald45k
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How to get genes within a GO category of 'GOstat' results?
... Hi All, I am using 'GoStat' package for GO enrichment analysis and so far I have been able to generate results from 'hyperGTest' without any issue. Here is my dummy code: top.genes = read.delim("Top200_others.txt") ## Test set ########### entrezTest.AF = top.genes[[1]] ## ENTREZ IDs ## Backgrou ...
go written 3.2 years ago by Bade310 • updated 2.9 years ago by Gordon Smyth32k
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Comment: C: Combing Effects (t-stats) from experiment with common reference design?
... Hi Ryan, Thanks for taking out time to reply to my question. I have samples from two tissues - Heart (20 different developmental stages) and Control (rest of the body, single fused sample from multiple time points). I performed 'limma' analysis (GLM approach) to identify up-regulated genes for each ...
written 3.2 years ago by Bade310
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Combing Effects (t-stats) from experiment with common reference design?
... Hi All, I was wondering whether there is any approach to combine 't-stat' from different comparisons but using same control. These are my contrasts: Stage1 vs ControlX Stage2 vs ControlX Stage3 vs. ControlX ......... Stage 20 vs. ControlX Here the control is same i.e. same sample for all contrast ...
written 3.2 years ago by Bade310 • updated 3.2 years ago by Ryan C. Thompson6.1k
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Error while mapping SYMBOLS to ENTREZID
... Hi All, I am getting a strange error converting Gene Symbols to Entrez ID. Here is my code: >testData = read.delim("IL_CellVar.txt",head=T,row.names = 2) > testData[1:5,1:3] ClustID Genes.Symbol ChrLoc NM_001034168.1 4 Ank2 chrNA:-1--1 NM_013795.4 ...
written 3.3 years ago by Bade310 • updated 3.3 years ago by Martin Morgan ♦♦ 20k

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Popular Question 20 months ago, created a question with more than 1,000 views. For Covariate for batch effect removal by ComBat

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