Questions tagged [edger]
The edger tag has no usage guidance.
42
questions
2
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1
answer
54
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DE analysis tool and method for non-coding features
I am currently working with the non-coding features of A. thaliana, and trying to get the DE features. Among the three DE test methods in edgeR such as ...
1
vote
1
answer
48
views
Filtering criteria for non-coding features with very low counts
I am trying to do DE analysis of non-coding features of A. thaliana. I find in the miRNA and lncRNA counts file that they are abundant in zero counts, and most of the non-zero counts are very low. Now,...
1
vote
1
answer
38
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Statistical methods suitable for DE analysis of non coding RNAs
I am currently working on DE analysis of coding as well as non-coding features of A. thaliana using the edgeR package.
Is the negative binomial method that is ...
2
votes
0
answers
46
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Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?
I am currently working on my PhD and as part of my thesis, I intend to analyse gene expression within multiple sclerosis (MS) lesions by looking at RNA-seq datasets on Gene Expression Omnibus (https://...
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2
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0
answers
34
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Does the contrast matrix I have made address the question I am trying to answer?
I have the following design matrix:
mm_noreps.interactions <- model.matrix(~condition*TRAPed)
Both variables are factors condition has 4 levels and TRAPed has 2 ...
- 376
0
votes
1
answer
84
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Batch correction in differential expression analysis
I have sent two sets (two batches in matter of sending for sequencing) of different samples (plasma) to small RNA-seq to Qiagen company
This is how my meta data look
...
- 1,981
3
votes
2
answers
362
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DESeq2 for large number of samples takes too much RAM
I am trying to run a very large number of transposase-accessible chromatin (ATAC)-seq samples through DESeq2 to find peaks of differential chromatin accessible across my study genome.
I have about 100 ...
1
vote
1
answer
84
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DESeq2 and EdgeR
I am new to using both DESeq2 and EdgeR in Bioconductor used for transforming my RNA expression data.
However, I am struggling to understand their specific purpose, differences between them and ...
- 13
1
vote
1
answer
195
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plotting gene expression after EdgeR DE analysis using RUVg (RUVseq) covariates
I have used the empirical RUVg method (from RUVseq) to estimate the unwanted variation of my dataset (consisting of several public datasets analysed together, with controls and case samples in ...
- 37
1
vote
2
answers
105
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Basic RNA Differential Expression in R
I have two matrices, one for individuals before treatment and one for the same individuals after treatment. Both matrices are raw read counts of RNA expression.
...
2
votes
1
answer
476
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What is the difference between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus for converting to gene symbols?
I am interested in the differences between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus. They yield the same results as seen in the code below.
...
- 165
2
votes
1
answer
445
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What is the difference between Normalized Expression in EdgeR vs DESeq2?
I am trying to access the normalized expression in both edgeR and DESeq2, yet the results are different. Does anyone know why?
How to get normalized expression using edgeR:
...
- 165
0
votes
0
answers
192
views
Differential miRNA expression using RPM
I have microRNA (miRNA) expression data in RPM. I would like to do differential gene expression between two groups.
How can I do this?
I have considered edgeR and DESeq2 in R, but it looks like they ...
- 257
0
votes
1
answer
577
views
RNASeq analysis using featureCount and EdgeR
I am using a pipeline (bam -> featurecount-> EdgeR) to do some RNASeq analysis of several groups and sub-groups. For example, I have the following dataset with two types (T1 and T2) and T1 has ...
- 195
0
votes
2
answers
207
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Determining what RNAseq data is filtered on volcano plot
I am using RNA seq data to analyze genes via a volcano plot comparing differential gene expression of bacteria with and without antibiotic in R. After having created my plot, I am unsure why some of ...
- 1
1
vote
2
answers
83
views
Bulk RNA-Seq Read Length Normalization across different samples
I have 20 samples out of which 14 are 100 bp in length and 6 are 150 bp. Is there a way to normalize the read length for cross-sample differential expression comparison? What would be the best way to ...
- 11
1
vote
1
answer
145
views
Why use "robust" FPKMs?
Both DESeq2 and edgeR have an FPKM/RPKM function that by default uses normalized library sizes ("robust" option in DESeq2). FPKMs have their own issues, but I thought the main benefit was to ...
- 2,169
0
votes
1
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82
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the variation between treatments is less than the variation between replicates in RNA-seq data
I have a set of RNA-seq samples from targeting different proteins in a complex with siRNAs. However, the ...
- 169
3
votes
1
answer
2k
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Removing Batch Effect in Heatmaps after Differential Gene Expression Analysis
I'm working on a dataset in which the first replicate of each group is one batch and the second replicate is in a second batch. After checking the PCA plot and ...
- 169
1
vote
0
answers
212
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Differential Gene Expression with Replicates for some of the samples
[this question has also been posted on Biostars; some additional clarification from there has been copied into this question]
I've been asked to analyse a set of samples in which their control sample ...
- 169
0
votes
0
answers
48
views
a proper Design Matrix for several drug treatments with both control negative and control positive
I have a dataset of RNA-seq samples for testing different drugs on the presence of another drug. One of my samples is the normal cells with no drugs (control negative) and another is the cells with ...
- 169
1
vote
2
answers
530
views
How to create a list of differentially expressed (DE) genes after normalization with RUVSeq?
I am using edgeR to perform differential expression (DE) analysis on a set of RNA-seq data samples (2 controls; 8 treatments). To correct for batch effects, I am using RUVSeq.
I am able to get a list ...
- 115
2
votes
1
answer
355
views
Comparing multiple treatments to multiple other treatments in edgeR for simple effects in a complex experimental design
I am working with a RNA-seq data set in maize that has a relatively complex design. There are two levels of treatment A (nitrogen fertilizer level in the field, high or low), two levels of treatment B ...
- 21
0
votes
1
answer
579
views
How to incorportate RIN values as covariate in the design matrix?
I have been following the last DESeq2 pipeline to perform an RNAseq analysis with a dataset with low rin samples in the experimental (or treated) and high rin on the control ones.
I read a paper in ...
- 37
1
vote
2
answers
41
views
Identify differentially covered genes only between two samples
I have a question about finding differentially covered regions (coverage represents methylation level which goes from 0 to several thousands). I'm using enrichment based method which can be summarized ...
- 203
2
votes
2
answers
218
views
What do these files / annotations mean?
I have no experience in Bioinformatics and I need to understand what the annotations given here mean (I am including the first few lines, please see the link for more):
...
- 187
0
votes
1
answer
209
views
RNA-seq: How to get new expression count after normalization
I've RNA seq, Human, Paired-end data, Sample size is <40. These are aligned using STAR, RSEM processed. With RSEM I've TPM and expected counts, that is two files columns as individual IDs and row ...
- 255
0
votes
1
answer
251
views
Correlate DEGs from DESeq2, EdgeR and Limma results
I have a lists of DEGs identified by DESeq2, EdgeR and Limma.
I would like to correlate the the gene rankings in the lists to decide on a package to use in downstream analysis.
I am havig a few ...
- 3
0
votes
1
answer
109
views
Single sample in group: normal pipeline or Kal's Z test
As stated, which one is better for differential expression analysis? When I say normal pipeline I mean limma-voom, edgeR and DESeq2 pipeline for standard analysis. Kal's z test is mentioned in this ...
- 105
1
vote
0
answers
428
views
What is the formula for Mg values in TMM normalization for RNA Seq data?
I am reading through the paper "A scaling normalization method for differential expression analysis of RNA-seq data" by Mark D Robinson, Alicia Oshlack, available here.
In this paper they introduce a ...
- 111
1
vote
0
answers
139
views
Gene ratio as imput in limma
I have a data frame with gene-expression ratio. Is it possible to input this into limma/voom to find signinficannt gene-ratios between groups of samples?
my data:
...
- 223
2
votes
1
answer
2k
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Calculating Z-score from logCPM values using edgeR
I have the raw counts for RNA-Seq data. I converted counts data to logCPM using edgeR package.
Lets say I have a dataframe A with 15000 genes as rows and 100 ...
- 1,262
0
votes
1
answer
76
views
Experimental Design for Differential expreression analysis
I have a Normal esophageal Fibroblasts (NOFs) cultured in DMEM media; The same NOF also have been cultured with a tumor sample from a patient named 005 on DMEM media; I have also Cancer Associated ...
- 1,981
1
vote
1
answer
406
views
Error in quantile.default(x, p = p) in EgdeR calcNormFactors
I am trying to run TMM normalization using rpy2 and when I run calcNormFactors() function:
<...
- 2,538
8
votes
1
answer
2k
views
How is prior.count used by edgeR's cpm
edgeR's cpm function has an argument called prior.count. Based on my understanding of the documentation, it is supposed to be adding a fixed number per sample which ...
- 183
0
votes
1
answer
2k
views
Batch Effects in RNA Seq Sample
I am using the R (using EdgeR) for the RNA Seq analysis, I had few batch effect samples like Control vs treatment. Could anyone tell me the best way to remove the batch effects.
I have looked into ...
- 23
1
vote
2
answers
3k
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How to calculate logCPM across all samples?
Using edgeR for differential analysis between Tumor and Normal gave me differential expressed genes with logFC, logCPM, PValue and FDR.
From the details of glmTreat function I see that logCPM is ...
- 1,262
1
vote
2
answers
1k
views
What could be the reason for the samples not clustering?
I'm performing RNA-seq analysis. I have used Hisat2 for aligning reads to the genome and stringtie for quantification and extracted read count information directly from the files generated by ...
- 1,262
2
votes
0
answers
2k
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Which R package to use for differential analysis with TPM values?
I'm using hisat2, stringtie tools for the RNA-Seq analysis. After stringtie using ballgown I get FPKM and TPM values for every gene.
I have seen that edgeR, Deseq2 can be used for Counts data. I ...
- 631
10
votes
2
answers
1k
views
*very* unbalanced group sizes for DE
I downloaded some publicly available RNA-seq data and want to compare those samples carrying a mutation (~4) against the rest (~800!). I ran both EdgeR and DESeq2, and the first results in an ...
- 405
8
votes
1
answer
405
views
When performing differential expression analysis, should genes with low read counts be removed before or after normalization?
I have RNA seq data which I've quantified using Kallisto. I'd like to use tximport to transform the read count data into input for EdgeR, following the R code supplied in the tximport documentation:
...
- 541
9
votes
1
answer
607
views
confidence ellipses for MDS plot in edgeR?
Is it possible to draw e.g. 95% confidence ellipses around samples from the same group on the results from the plotMDS function under edgeR? If so, how?
- 153