Questions tagged [linear-regression]

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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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3answers
65 views

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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0answers
18 views

Filtering criteria for selecting DEGs from Monocle3 regression analysis with categorical terms

I'm testing the package Monocle3 (version 0.2.0) with the following code. The main aim of this analysis is to identify differentially expressed genes for every time ...
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0answers
20 views

How can I perform the assumption of the lmfit function from limma package?

I'm doing a DNA methylation analysis using the limma package. The idea is to explore if there is a dose-response between exposure (pm2.5) and methylated CpG sites. Here is my code. I would like to ...
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0answers
43 views

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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0answers
26 views

Trouble optimizing Five Parameter Logistic (5PL) Standard Curve for ELISA data using Python

I am attempting to write a tool to be used by my lab to automatically generate 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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1answer
46 views

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 ...
1
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1answer
116 views

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 ...
2
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2answers
70 views

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 ...
2
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1answer
65 views

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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0answers
90 views

Several models identify different which genes are significant

I want to find some good predictors (genes). This is my data, log transformed RNA-seq: ...
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3answers
779 views

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, ...
5
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1answer
180 views

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: ...