Questions tagged [linear-regression]
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MLPE in lmer (lme4 in R)
I am trying to conduct some landscape genetics analysis by testing association between landscape resistance matrices and pairwise genetic distances using linear mixed models. When I run lmer package, ...
Advise on building an effect ML model for predicting important proteins for drug response
I want to create a model to predict proteins which could be associated with drug response in cancer cell lines. I have cell line proteomics data, with compound screening data they have gained for a ...
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 ...
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 ...
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 ...
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 ?
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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, ...
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: ...