Questions tagged [edger]
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23
questions
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40 views
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 ...
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0answers
26 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 ...
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2answers
56 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 ...
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1answer
21 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 ...
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1answer
46 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 ...
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2answers
32 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 ...
2
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2answers
208 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):
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1answer
57 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 ...
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1answer
128 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 ...
0
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1answer
50 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 ...
1
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0answers
271 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 ...
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0answers
76 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:
...
1
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1answer
558 views
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 ...
0
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1answer
69 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
vote
1answer
183 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:
<...
6
votes
1answer
600 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 ...
0
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1answer
833 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 ...
1
vote
1answer
1k views
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
vote
2answers
304 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 ...
2
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0answers
905 views
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 ...
10
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2answers
615 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 ...
8
votes
1answer
349 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:
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9
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1answer
319 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?
