User: jhj89

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jhj8910
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Posts by jhj89

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WGCNA comparing and contrasting two networks
... I am not sure whether this type of post is appropriate but I couldn't get a straightforward answer so here goes: I am currently following this tutorial (https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/WORKSHOP/2013/Miller/Miller1_ComparingMouseAndHumanBrain.pdf) that enables comparing an ...
wgcna written 3.0 years ago by jhj8910
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Comment: C: Correlation analysis taking into account multiple correlations
... Thanks Aaron, So if I take a GLM approach (with glmFit and glmLRT), it would give me raw p-values and the FDR values for each of the associated genes). If I understand correctly, multiple test correcting can be done by taking the raw p-values from all comparisons and do the adjustment (with p.adjus ...
written 3.1 years ago by jhj8910
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Correlation analysis taking into account multiple correlations
... Hi, I have previously asked a question about doing correlation analysis between host genes and pathogen genes. (https://support.bioconductor.org/p/80545/). One of the possible approaches was taking a GLM approach to compare one gene (from the host) to all the genes (from the pathogen) at a time, an ...
edger rna-seq correlation written 3.1 years ago by jhj8910 • updated 3.1 years ago by Andrew_McDavid190
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Comment: C: including information indicating upregulation/downregulation of genes in goana()
... Dear James and Gordon, Thank you so much! I got it to work. ...
written 3.1 years ago by jhj8910
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including information indicating upregulation/downregulation of genes in goana()
... Hi, To put it simply, I have a list of genes with information about whether they are upregulated or downregulated. What should the format of the input be when using goana() such that I can include the information about upregulation or downregulation of each of the genes? I understand that goana() c ...
edger goana written 3.1 years ago by jhj8910 • updated 3.1 years ago by James W. MacDonald51k
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Comment: C: Co-expression between host and pathogen genes
... Thank you. Just one more question: if there are multiple covariates that I want to adjust for, and if I have them in a matrix (ex. multiple_covariates), would the following work in the same way as having just one covariate (ex. Age)? logCPMs <- removeBatchEffect(logCPMs, design=subdesign, covar ...
written 3.5 years ago by jhj8910
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Comment: C: Co-expression between host and pathogen genes
... Thank you Aaron for your answer. I have a slight off-topic question but it is something related to what I have above. I am wondering whether it would be possible to extract logCPM from edgeR that takes into account the covariates such as Age. For example, if I were to use WGCNA package, it requires ...
written 3.5 years ago by jhj8910
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Comment: C: Co-expression between host and pathogen genes
... Thank you for your answer. I tried your approach and it works quite well. ...
written 3.5 years ago by jhj8910
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Co-expression between host and pathogen genes
... Hi, I have this host and pathogen RNA-seq data generated from the same individuals and I have performed DGEA on both data to determine the DE genes between two disease groups. With this, I would like to find out which host DE genes are correlated with which pathogen DE genes. I thought a simple pea ...
edger rna-seq written 3.5 years ago by jhj8910 • updated 3.5 years ago by Aaron Lun25k
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Comment: C: Effects of continuous variable with adjustment for gender
... Thank you for your answer: Just a side question: I was reading this post from biostars (https://www.biostars.org/p/143988/) and I was wondering how should I treat the continuous variable being included in the model. Should I include as it is, or log-transform them? I guess it kind of makes sense to ...
written 3.6 years ago by jhj8910

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