Questions tagged [pca]

Question 1

I am taking my first course in bioinformatics, and as such I am quite the beginner. This week we've discussed relative log expression, centered log ratio, and using those methods to normalize the data ...

Question 2

This question was also asked on Reddit I am trying to perform SVD on gene expression data (Genes in the rows and samples in the column). I begin with row centering of the data. Then I do column ...

Question 3

I am working with scRNA data that I reduced to the 100 High Variance Genes and using UMAP to visualize it in 2D. Before applying UMAP, I perform PCA for dimensionality reduction. I am trying to decide ...

Question 4

I am working with Single-Cell RNA-seq count matrices (gene expression x cells) from multiple files, which represent different samples and patients. I want to perform dimensionality reduction using PCA ...

Question 5

I have genomic data for already converted in eigensoft format. Specifically I have SNP data for 5 populations and 1 outgroup. I ran smartpca with the following ...

Question 6

I wanted to help out a colleague and I wanted to know if the things I'm doing are making sense-ish. The data consists of tissue sections which had been stained for markers. The tissue segments are ...

Question 7

I would like to get a pca plot from the multiple sequence alignment (fasta file). I extracted snps in vcf format using snp-sites program. ...

Question 8

This question was also asked on Reddit I am new to sc-rna analysis, I have the dataset that I am trying to find out the best UMAP, experimented on trying out different values of the parameters as in (<...

Question 9

I am very new to analyzing RNAseq and I am in a group with very little experience in this regard and I am looking for some advice. My PCA after performing DESEQ2 analysis on my dataset doesn't show ...

Question 10

I have done miRNA sequencing from animal tissue and have control sample in duplicates . Like wise one treatment group as test. In PCA plot clustering is not there. There is very randomness. Is it ...

Question 11

Utilizing a reference panel, I want to assign most likely population label to each individual in the study. Following are the files I have: Reference panel population labels: ...

Question 12

I'm trying to perform Principal Component Analysis using R on a proteomics dataset. As the dataset contains a lot missing values I tried different approaches. I ran PCA using ...

Question 13

I am new to the scRNA-seq field and I have been doing some experiments of visualization of UMAP using different numbers of PCA components for initialization. The process involves projecting scRNA-seq ...

Question 14

I've got a moderately large set of PBMCs, over 1M cells. That means I can't easily do a grid search of dimensionality reduction/clustering parameters/methods. Some examples results I'm getting with ...

Question 15

Sorry if the answer to this should be obvious. I have RNA-expression results from 24 samples which can be divided into 6 groups, (wildtype and two different mutants at two different ages) with a total ...

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Questions tagged [pca]

Linearization versus Normalization when it comes to omics data

SVD on gene expression data

Optimal PCA Dimensionality Reduction Before UMAP for 2D Visualization of High-Dimensional Data

Should I apply PCA on the combined scRNA dataset or on each individual file?

How can i resolve "too many entries" error in EIGENSTRAT?

Plotting PCA from cell counting data, viable way for analysis?

pca plot from multiple sequence alignment

How can I quantitatively evaluate which UMAP is best in terms of clustering & embedding?

PCA of bulk RNA-seq doesn't show clustering and show large variation in general

Done miRNA sequencing from animal tissue & have 1 control sample in duplicates 1 treatment group as test. In PCA plot clustering is not there

Predict population based on PC coordinates

How to perform PCA on proteomic data set

Question about umap using different numbers of pca components as initialization

scRNA: What are good dimensionality reduction/clustering parameters to get biologically plausible groupings?

Test for differences between groups of samples

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