Questions tagged [linear-regression]

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Extracting adjusted expression after adjusting for covariates

For a given number of features (hundreds ~ thousands protein quantifications) and samples (hundreds) I am fitting a multi-linear model where I am aiming to regress out the effect of a few covariates. ...
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Inflated p-values in quantitative trait analysis

I am performing a quantitative trait association between the expression of one gene and ~400,000 methylation values. First, both variables are rank inverse normal transformed, adjusted for confounders ...
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Model the effect of treatment on mutation burden

I am struggling a bit to model the following problem. Basically, I would like to model tumor mutation burden (mutations per megabase, a continuous) as a function of treatment (categorical). The ...
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GWAS, MWAS, EWAS: what are the (in)dependent variables?

I started reading some papers on X-wide association studies, where X can be metabolome, epigenome, etc... The authors usually describe which are the dependent and which are the independent variables ...
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What is the difference between fixed effects and random effects in the context of Linear-mixed models?

The terms in LME i.e. fixed and random create confusion? What is the genesis that can distinguish between the two ?
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Detect differentially expressing cells

after comments on my original post, I will ask my question again here I have data (RNA expression values, obtained with multi-channel in situ hybridization) collected from 1mio human cells. For each ...
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Trouble optimizing Five Parameter Logistic (5PL) Standard Curve for ELISA data using Python

I am writing a Python script to automate a 5PL Standard Curve for ELISA data, using an XLSX file template. I am using pandas dataframes to hold the 96 wells as ...
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1 answer
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Can I use a regular liner regression model when I'm working with DNA methylation data?

I'm new on working with genetics data and I'm just wondering if I can use the lm function when I'm building my models or do I have to use ...
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Doing plot with this data

I have normalized expression values of some genes in some patients and the how many days they have survived from their diagnosis with cancer like below EDITED I have taken mean of the expression ...
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2 votes
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How do I Investigate and test the hypothesis on the effect of street-light regime on insects?

I need advice on a suitable analysis of a dataset that has an akward design because we investigate a real-world situation. We have two sites (A, B) where we can conduct the research. The hypothesis ...
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2 votes
1 answer
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How are residuals used as new phenotype?

I'm a novice trying to wrap my head around with fancy jargons. If I search residual, I understand that it represents the difference between the observed value of the dependent variable (y) and the ...
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3 votes
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114 views

How do I resolve disagreements in the determination of significant genes?

I want to find some good predictors (genes). I have checked the Spearman correlation of the expression of each of 23 genes with dependent variables (responders Vs non-responders and I saw only the 5 ...
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Regressing out unwanted sources of variation in single cell RNA-seq data

I have a dataset of single cell count data and I want to regress out the variation caused by the number of UMI's and the percentage of mitochondrial genes. I know that count data is discrete data, ...
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Scaling by linear regression against the number of reads

I am trying to build the preprocessing pipeline presented in The Tabula Muris Consortium et al. (pp). It is a pipeline to preprocess single-cell sequencing data. There is one step that is not clear: ...
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