User: hamaor

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hamaor0
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Posts by hamaor

<prev • 6 results • page 1 of 1 • next >
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Error while annotating with Chipseeker
... I followd the Diffbind pipeline for a ChipSeq data: peaksets2 = dba(sampleSheet="SampleSheet.csv",config = data.frame(RunParallel=TRUE, AnalysisMethod=DBA_DESEQ2, bCorPlot=FALSE, bUsePval=TRUE, minQCth=10),minOverlap = 2) peaksets2 <- dba.count(peaksets2) peaksets2 <- dba.con ...
chipseq annotation written 29 days ago by hamaor0
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how to retrieve binding affinity matrix in diffbind
... hey everyone, I'm performing ChIP-Seq analysis using diffbind, after doing: > dba.count(peaksets, summits=250) I would like to get the binding affinity Matrix into a text file. help will be highly appriciated!! ...
diffbind dba.count written 4 weeks ago by hamaor0 • updated 4 weeks ago by Rory Stark2.7k
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Comment: C: is it possible to create this comparison?
... hey Erin,  it seems that it answers the pairwise comparisons of the effect of the treatment for each genotype, or the genotype gene expression on the same treatment.  what i'm trying to do is to mix between different levels of each factor. so if i have genotype I,II and treatment A,B i'm looking f ...
written 3.1 years ago by hamaor0
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is it possible to create this comparison?
... i'm using deseq2 for my RNASeq analysis. i have 2 factors, each has 2 levels: 1. genotype : col (wildtype), M6_5 (mutant) 2. treatment: Nacl, control my design is: ~ genotype + treatment + treatment:genotype. to get the effect of the treatment for each genotype i used: results(dds, contrast = ...
rnaseq deseq2 multiple comparisons pairwise written 3.1 years ago by hamaor0 • updated 3.1 years ago by Michael Love22k
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Comment: C: how to deal the effect of enormous gene expression?
... just to clarify, we have 2 time point: T0 and T5 (right after heat shock, and 5 hours after heat shock respectively) , when the heat shock effect is much more significant in T0 when small subset of genes have great expression level.  is it possible that genes that showed positive fold change in T5 ...
written 3.1 years ago by hamaor0
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how to deal the effect of enormous gene expression?
... Hey everyone, this is my first question in the forum.  i'm analyzing RNA-Seq data of Tomato.  some of the samples were treated with HeatShock, and comparing to the control groups it seems that  a small group of genes presenting enormous values of expression.  my question how does it effects oth ...
geneexpression rnaseq deseq2 tomato written 3.1 years ago by hamaor0 • updated 3.1 years ago by Michael Love22k

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