User: teabonng

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teabonng10
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Posts by teabonng

<prev • 8 results • page 1 of 1 • next >
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Gene expression meta analysis
... Hi, I am analyzing independent RNA-Seq datasets and doing a meta analysis. Is it valid to compare global transcription profiles from multiple datasets based on the fold changes? For each RNA-Seq dataset, I normalize counts within each dataset and then calculate the fold changes of all genes relativ ...
transcription profiles gene expression written 1 day ago by teabonng10
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Identification of co-regulated genes by clustering
... Hi, I would like to identify clusters of co-regulated genes based on gene expression data under various treatment conditions. I am wondering how many of these treatment conditions, like how many experiments/datasets are needed to reliably determine these clusters. Will 10 datasets be enough? Thank ...
gene expression co-regulated genes clustering written 7 days ago by teabonng10
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Comment: C: edger model matrix design of linear model
... Hi, there is a big difference in the results. The results using the design <- model.matrix(~timepoint) makes much more biological sense. ...
written 10 days ago by teabonng10
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Comment: C: Train classifier based on unsupervised clustering of genes
... Hi Jean-Karim, Thank you very much for the insights. The important features are what we aim to determine. So , when we get a good performing machine learning model, maybe we can get the top features based on the coefficients. ...
written 10 days ago by teabonng10
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edger model matrix design of linear model
... Hi, I am trying to do differential expression based on RNA-seq data. I only have one variable, which is the timepoint. I want to analyze gene expression relative to the 0 h time point. I already set up the contrasts. Now, I am trying to set up the design matrix. What is the difference between desi ...
design matrix edger differential expression written 10 days ago by teabonng10
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Train classifier based on unsupervised clustering of genes
... Hi, I will be training a classifier based on the results of unsupervised clustering of genes. The overall goal is to determine which chromatin or epigenetic features in these genes are the best features indicating that they are regulated by a central protein regulator. First, I will cluster genes ...
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Comment: C: edgeR - normalized counts from multiple datasets
... Thank you very much for your answer and recommendation. ...
written 11 days ago by teabonng10
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edgeR - normalized counts from multiple datasets
... Hi, I am combining multiple independent rnaseq datasets from the same species but different conditions and analyzing them together. I normalized the counts per dataset using calcnormfactors in edger. I will have to do a second normalization when the different datasets are combined. I rounded up th ...
normalization rna-seq edger written 15 days ago by teabonng10 • updated 9 days ago by 15617759110

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