Tag: log2FoldChange

InteractiveComplexHeatmap on DESeq2 object with more than 2 groups

InteractiveComplexHeatmap on DESeq2 object with more than 2 groups 1 Hello all, I’m writing with the hope someone can clarify a doubt I have about the differential heatmap generated by the package InteractiveComplexHeatmap via the simple command interactivate(dds). I read the package documentation at bioconductor.org/packages/release/bioc/html/InteractiveComplexHeatmap.html, but I couldn’t find the…

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Genes looking differential abundant are not accoring to DESeq2

Genes looking differential abundant are not accoring to DESeq2 0 I have a metagenomic dataset crossing three time points from which I have mined CAZymes and am using DESeq2 to identify differentially abundant CAZymes from using trimmed mean depth generated my CoverM (very similar to Q2Q3 contig coverage). From this…

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Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold

I have a result from which I want to get significant genes (pvalue-threshold=0.1, log2FoldChange threshold 1.5), and divide them into up-regulated and down-regulated. From the vignette, I found the following on down-regulation and up-regulation: subset the results table to these genes and then sort it by the log2 fold change…

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r – Filtering data and labeling them based on threshold issue

I’m trying to set a threshold with different criteria to label data points into categories So my code is this C1_C2 = read.csv(“C1_C2_contrast.txt”) diff_C1_C2 <- C1_C2 %>% mutate(UP_DOWN = case_when( # padj < 0.05 & log2FoldChange > 1.5 & log2FoldChange < 2.5~ “UP”, baseMean > 50 & pvalue < 0.05…

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Fatty infiltration after rotator cuff tear

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

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How to do functional analysis on differentially expressed gene list from RNA-seq data?

How to do functional analysis on differentially expressed gene list from RNA-seq data? 0 @06f08eeb Last seen 1 day ago Canada Hi all, I am a complete beginner in terms of bioinformatics analysis and I am hoping to complete some functional analysis on some differentially expressed gene lists of some…

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Strangely too low P-value and Adjusted P-value(FDR) DESeq2 and edgeR

My data is experimental data that has been overexpressed for a specific gene. Data samples are divided into 3 groups according to the over-expression time and each group has 3 samples. (total 9 samples) I conducted DGE analysis on the control group and one case group with DESeq2. cts <-…

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Change log2FoldChange range – plotMA

You can use base R graphics to make these plots. The data is sitting there in columns of the res object, so you can filter it directly, and use boolean vectors to pick out the things you need: # make sure there are no NA values sum(is.na(res$log2FoldChange)) # choose some…

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sigh of log2FC values in DESeq2

sigh of log2FC values in DESeq2 0 @194b0276 Last seen 10 hours ago United States Can someone explain to me how is the sign of log2FoldChange is set in the results of DEseq2? I was pretty sure that it is calculated as log2(Counts_treatment/Count_reference), where reference is determined alphabetically (unless specified…

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highlighting specific genes (from a user-supplied list) in a Volcano plot in R

highlighting specific genes (from a user-supplied list) in a Volcano plot in R 1 I’ve generated a volcano plot using DeSeq2 results and would like to specifically highlight a subset of genes by providing a list of gene IDs Dataset$condition <- relevel(Dataset$condition, “Ctrl”) res <- lfcShrink(DatasetProcessed, contrast=c(“condition”,”Treat”,”Ctrl”)) with(res, plot(log2FoldChange, -log10(pvalue),…

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TPM value from DESE2 and significant filterig isssue

TPM value from DESE2 and significant filterig isssue 0 The code 10101 res_ddsDE_new has 36,000 rows. When I am using subset(res_ddsDE_new, padj < 0.05 & abs(log2FoldChange) > 1) res_ddsDE_new baseMean log2FoldChange <numeric> <numeric> DDX11L1 1.779144 -1.4955939 WASH7P 152.518293 -0.0505911 MIR6859-1 20.653876 0.5689275 MIR1302-2HG 0.255387 -1.9691031 FAM138A 0.353478 0.1574042 Then I…

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Understanding the output of Negative Binomial in DESeq2

Are zero is a default option of log2fold change to be considered as up and down? Yes, by default, the null hypothesis is that the log2FoldChange is zero. Does this mean that there are seven genes in total that will have significant adjusted p-value? Yes, you are interpreting your results…

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DESeq2 log2FC and p-value filtering

DESeq2 log2FC and p-value filtering 1 Dear all, I want to filter DE genes by log2FC > 2/-2 and p-value 0.0001. Why this two versions of lof2FC and p-value filtering differ in up- and down-regulated genes numbers (from 800 to 1500) and which one is the right one ? 1….

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Correct way to make multiple comparisons on DESeq2?

I have a project where I have done RNA-seq (paired-end sequencing on Illumina HiSeq) of a worm at different days of development i.e. Ages 0-12. For each age, I have sequenced 3 replicate specimens. I’m new to DESeq2 and I was wondering if what I did below is correct. library(DESeq2)…

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Outliers on DESEq2 Results

I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from 10 to 12, with a few counts > 9000. I process this data in Deseq2 and get that the gene is differentially expressed across several samples of interest. What can…

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Need help to remove NA values from data frame

Need help to remove NA values from data frame 2 I have this data frame : and I want to remove those rows which contain NA values from the log2fold change column How can I do this through R? DeSEQ2 R • 256 views Hi Anas, If your data frame…

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Volcano plot not centered at origin

I am making a volcano plot for my phosphoproteomics data and seemingly the data are not centered around the origin. The reason that I know there is something wrong is because before my code was producing the correct volcano plot, and now it is shifted. What are some reasons why…

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Handle inflated log2FC while using interaction term in DESeq2

Hi guys, I’m working with a 8 samples experiment (lower than 3x replicates, I know..) with a design like > colData(dds) DataFrame with 8 rows and 2 columns condition traitment <factor> <factor> 4200-JS-1 norm ctrl 4200-JS-2 norm ctrl 4200-JS-3 norm trt 4200-JS-4 norm trt 4200-JS-5 hyper ctrl 4200-JS-6 hyper ctrl…

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Is it a good idea to plot a volcano plot starting at position x =1

Is it a good idea to plot a volcano plot starting at position x =1 1 Hello everyone! I was wandering if it makes sense to start a volcano plot (x=log2FoldChange) starting at position one, so basically discarding all values below 1 and above -1 leaving only values outside this…

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Circos plot with logfold change RNA seq data

I am new to circos plot analysis and have been trying to use the cyclize package. I want to display mRNA differential gene expression data based on data analyses of 8 libraries and links between their respective target genes. The dataset I am working with looks like this geneid baseMean…

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lfcShrink probelm in many 0 count genes RNA-seq data

Hi, Dr love. I post a question about weird MAplot or volcano plot of DESeq2 diff result and also in biostar. ATpoint give a useful answer about too many 0 count genes and prefiltering. It seems that too many 0 count genes makes lfc shrink have a probelm. And I…

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weird MAplot or volcano plot of DESeq2 diff result

Hi, every one. I find a werid MAplot or volcano plot of DESeq reuslt. I am wondering whether you can give me some advice. This diff result is from two cell type bulk RNA-seq. I use two specific marker to get these two cell type using Flow cytometer. I alreadly…

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same padj for all the genes after DEseq analysis

Hi everyone, I have done a pair comparison with DEseq2 to find differentially expressed genes between two samples with 6 replicates, for the DEseq2 result, i got exactly same padj value for all the genes and it is not significant, is this normal ? I don’t think the padj should…

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