Showing : counts • reset
0
votes
2
replies
169
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 6 months ago by 32k • written 6 months ago by • 0
1
vote
8
replies
192
views
[Outlier Gene removal] - One sample with outlier counts for some genes
RNAseq DESeq2 outlier counts DE analysis
updated 11 months ago by 2.8k • written 11 months ago by • 0
2
votes
4
replies
759
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
2.0 years ago • updated 13 months ago Mozart ▴ 20
0
votes
0
replies
187
views
using gene expression matrix for TCseq package to cluster genes
TCseq microwarray cluster counts normalization
21 months ago bioyas • 0
5
votes
3
replies
355
views
Combining counts from non-replicate samples in RNA-Seq analysis for a synergistic system
edger normalization counts RNA-seq
updated 22 months ago by ★ 26k • written 22 months ago by • 0
2
votes
1
reply
329
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 2.1 years ago by ★ 3.8k • written 2.1 years ago by ▴ 10
0
votes
4
replies
3.0k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 2.1 years ago by • 0 • written 2.4 years ago by • 0
0
votes
7
replies
379
views
Results table completely wrong for specified contrast of
DESeq2 logfoldchange counts
updated 2.3 years ago by 32k • written 2.3 years ago by ▴ 40
0
votes
7
replies
661
views
Count filter for differential expression
edger limma counts
updated 2.4 years ago by 42k • written 2.4 years ago by • 0
2
votes
4
replies
415
views
why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
deseq2 edger fpkm counts fc
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
1
vote
2
replies
384
views
how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
deseq2 edger fpkm counts TCGA
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
0
votes
3
replies
868
views
Handling pseudogenes in RNA-seq
rna-seq pseudogenes STAR counts
updated 2.9 years ago by 1.1k • written 2.9 years ago by • 0
2
votes
3
replies
646
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
written 3.0 years ago by ▴ 10
1
vote
1
reply
367
views
How to compare RNA-seq counts matrices from different aligners ?
rnaseq counts alignement
3.1 years ago Aurora ▴ 10
2
votes
3
replies
1.1k
views
Deseq2: padj value changes with varying alpha
deseq2 counts rnaseq
updated 3.5 years ago by 32k • written 3.5 years ago by • 0
0
votes
5
replies
2.2k
views
unable to find an inherited method for function counts for signature DESeqTransform
deseq2 counts DESeqtransform variance deviation
updated 3.6 years ago by 32k • written 3.6 years ago by • 0
0
votes
3
replies
596
views
DESeq2 ComputeSumFactors extract normalized counts
deseq2 normalization counts
updated 3.6 years ago by 32k • written 3.6 years ago by • 0
0
votes
0
replies
453
views
Combined strand specific and unstranded samples
strand rnaseq differential gene expression batch effect counts
3.6 years ago lirongrossmann ▴ 60
4
votes
2
replies
1.1k
views
Help: extract counts from RNA-seq .bam/.bai files
counts edger
updated 4.0 years ago by ★ 26k • written 4.0 years ago by ▴ 60
6
votes
4
replies
2.2k
views
Can edgeR TMM normalization be used for other count data?
edgeR tmm normalization counts
updated 4.0 years ago by 56k • written 4.0 years ago by ▴ 40
0
votes
1
reply
866
views
IRanges object from count matrix
genomicranges iranges featurecounts counts rnaseq
updated 4.2 years ago by 14k • written 4.2 years ago by ★ 1.5k
0
votes
2
replies
564
views
small RNAs quantification
smallrna counts
4.6 years ago ribioinfo ▴ 90
2
votes
1
reply
1.9k
views
DESeq2 Input format
deseq2 counts
updated 4.6 years ago by 32k • written 4.6 years ago by • 0
1
vote
3
replies
751
views
DESeq2: Do basemean values take into account interaction effects?
deseq2 counts normalized counts
updated 4.8 years ago by 13k • written 4.8 years ago by ▴ 40
2
votes
1
reply
858
views
converting extremely sparse count dataframe to continuous distributions for study in WGCNA
limma voom voom counts
updated 4.8 years ago by 42k • written 4.8 years ago by ▴ 50
1
vote
4
replies
590
views
comparing transcripts expression between conditions
salmon transcripts significance counts
4.8 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
835
views
Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, can I calculate error for counts values from lfcse output?
deseq2 chipseq counts log2fc error
updated 4.9 years ago by 32k • written 4.9 years ago by • 0
3
votes
1
reply
681
views
window counts in csaw
csaw counts
updated 5.0 years ago by ★ 26k • written 5.0 years ago by • 0
6
votes
12
replies
6.8k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 5.0 years ago by 32k • written 5.0 years ago by ▴ 10
4
votes
3
replies
4.1k
views
How do I extract read counts from DESeq2
deseq2 counts covariates
updated 5.2 years ago by 32k • written 5.2 years ago by ▴ 10
1
vote
3
replies
1.8k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools deseq2 counts cuffdiff
5.2 years ago Jon Bråte ▴ 180
2
votes
4
replies
1.4k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
5.3 years ago bioprog • 0
2
votes
5
replies
2.1k
views
Limma/DESeq2: Statistic and readcount of biological replicates
normalization limma deseq2 counts
updated 5.3 years ago by ★ 26k • written 5.3 years ago by ▴ 80
1
vote
5
replies
1.1k
views
deseq2 normalized data
regression deseq2 counts
updated 5.6 years ago by 32k • written 5.6 years ago by • 0
0
votes
1
reply
4.1k
views
Not full rank design using Deseq2
deseq2 design counts
updated 6.2 years ago by 32k • written 6.2 years ago by ▴ 20
0
votes
1
reply
854
views
DEXSeq error: Count files do not correspond to the flattened annotation file
DEXSeq counts gff
6.5 years ago Assa Yeroslaviz ★ 1.5k
3
votes
5
replies
5.7k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 6.5 years ago by 13k • written 6.5 years ago by ▴ 10
37 results • Page 1 of 1
Recent ...
Replies
Comment: Limma paired analysis design question by jefflincoln4 • 0
Thank you Gordon. One more thing, why use the log of blood iron concentration?
Answer: Limma paired analysis design question by Gordon Smyth 42k
Just put (log) blood iron concentration and `pair` in the design matrix. limma will work with differences automatically -- there's no need…
Comment: Extracting the findPalindrome() results by Hervé Pagès 14k
Also, you have a point: the output of `Biostrings::findPalindromes()` is an XStringViews object and `as.data.frame()` does a poor job on th…
Comment: Compute fgsea with my own database with R version 4.0.2 by assaron ▴ 190
I'm not sure what would be the best course of action in your case, if there is one at all, but I'd suggest to keep the ranking on the gene-…
Comment: Error installing Deseq2 by ATpoint ▴ 590
Go through the error logs and find the first error, this is where you have to start debugging, this here is just the consequences of the in…
Votes
Comment: DESeq2 with high range of within-group variability
Comment: problem regarding differential gene express analysis
Comment: Normalisation in DESeq2
Answer: Compute fgsea with my own database with R version 4.0.2
Comment: lmFit, number of proteins
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