Questions tagged [fold-change]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1 vote
2 answers

Gene list from eclip-seq .bed files

I have some eclipseq data, three IP and three input datasets, and have the alignments for all three. I used Bedtools "Intersect Interval" with the genome gtf file (hg19) I used to align them ...
user18763's user avatar
1 vote
0 answers

Manually calculating log2 fold change values from DESeq2 normalized counts [closed]

This question was also asked on Biostars and Bioconductor Support My aim is to perform gene clustering based on RNA seq datasets (raw expression values) from NCBI database. After clustering I realized ...
jayesh kumar's user avatar
1 vote
0 answers

How to compare Log2 Fold Change values

I have 5 sets of Log2 Fold Change values pulled off DualSeqDB. Each of the 5 groups corresponds to a different microbial taxon. Within the 5 groups, there are many Log2 Fold Change values, each ...
pythonbeginner44's user avatar
0 votes
1 answer

Doubt about using TPM for statistics

We designed an experiment to explore the potential role of carbon dioxide on algae physiology using RNA-Seq. We analyse the differential gene expression using DESeq2 but now we are interested into ...
Manuel Sánchez Mendoza's user avatar
0 votes
1 answer

Clustering RNAseq fold-change data

I have a dataset that looks something like this Treatment1 Treatment 2 Control Sample1 3.23. 0.87. 1 Sample2 1.71. 1. 1 Sample3 2.88. 5.65 1 Sample4 0.77. 1.34 1 The numbers describe a fold ...
Anonymous Scientist's user avatar
2 votes
1 answer

How to calculate fold change in gene expression from RSEM (RNAseq)

I have gene expression data from RNAseq, specifically: log2(x+1) transformed RSEM normalized counts. How can I convert these data from multiple samples to determine fold change in gene expression?
Sylvia Rodriguez's user avatar
3 votes
3 answers

Normalization for two bulk RNA-Seq samples to enable reliable fold-change estimation between genes

I have two bulk RNA-Seq samples, already tpm-normalized. I would like to know what is a reasonable normalization procedure to enable downstream log fold-change estimation. The distribution of the ...
gc5's user avatar
  • 1,783