User: tolgaturant

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tolgaturant20
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Posts by tolgaturant

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Find all genes that significantly correlate with a particular geneA?
... I want to use DESeq2 for normalization across samples. Plus I have other comparisons that included 2 conditions where I used DESeq2 on the same dataset. So if it is possible to use DESeq2 for gene to gene correlation I want to use DESeq2 normalization here as well. ...
written 23 months ago by tolgaturant20
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Comment: C: Find all genes that significantly correlate with a particular geneA?
... GC content normalization can be performed because of the biases during PCR amplification and library prep. So if a gene is detected less because it has very high or very low GC content, that might be problem when compared to other genes. The GC content normalization is not done to correct for the h ...
written 23 months ago by tolgaturant20
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Comment: C: Find all genes that significantly correlate with a particular geneA?
... Thank you very much, I will try WGCNA and compare with DESeq2! ...
written 23 months ago by tolgaturant20
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Comment: C: Find all genes that significantly correlate with a particular geneA?
... That's exactly what I want to do. But should gene length and GC content be an issue? ...
written 23 months ago by tolgaturant20
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Comment: C: Find all genes that significantly correlate with a particular geneA?
... Thank you for your answer. It is the first one. I am interested in gene to gene correlation without considering any case vs control model. For example in a clinical dataset from a uniform cohort, what genes are high when gene of interest is high or low when gene of interest is low. My question is ca ...
written 23 months ago by tolgaturant20
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Comment: C: Find all genes that significantly correlate with a particular geneA?
... Hi theobroma22 , That's why I am asking. As far as I know DESeq2 normalizes across samples but does not normalize for gene length or GC content with the rationale that every gene is modeled separately. There are other packages which do normalize across genes, such as EDAseq or FPKM. Should I use the ...
written 23 months ago by tolgaturant20
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Comment: C: Find all genes that significantly correlate with a particular geneA?
... Thank you. Are you referring to principle component analysis? Plotting and reducing the data would also help but I am looking for pvalues and estimates for each gene in the dataset. I am assuming some genes will significantly correlate with geneA and others will not. My questions is if such model is ...
written 24 months ago by tolgaturant20
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Find all genes that significantly correlate with a particular geneA?
... Hello, I want to find all genes that positively or negatively correlate with a particular gene A in an RNA-seq dataset. Can I use the normalized expression values of gene A as a continuous variable and perform expression profiling using DESeq2. Would gene length and GC content be an issue in such a ...
continuous variable deseq2 correlation rna-seq written 24 months ago by tolgaturant20 • updated 24 months ago by theobroma221.1k
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Comment: C: Combining control samples from 2 separate studies. Model matrix for batch effect
... Thank you for confirming. Could you suggest a reading that explains what the additional variables in the design are doing and when the model is not full-rank? ...
written 2.1 years ago by tolgaturant20
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Combining control samples from 2 separate studies. Model matrix for batch effect?
... For a gene expression project using limma, I have 2 studies with control samples processed the same way but at different times. However, the treatment samples are coming from only one study. I did not want just pool the controls, instead wanted to add the controls with a batch variable. Is below mod ...
R limma gene expression model matrix batch effect written 2.1 years ago by tolgaturant20 • updated 2.1 years ago by Devon Ryan88k

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