Showing : counts • reset
6
votes
12
replies
17k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 8.0 years ago by 41k • written 8.0 years ago by ▴ 10
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 6 months ago by • 0 • written 5.4 years ago by • 0
4
votes
3
replies
9.4k
views
How do I extract read counts from DESeq2
deseq2 counts covariates
updated 8.1 years ago by 41k • written 8.1 years ago by ▴ 10
3
votes
5
replies
8.5k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 9.5 years ago by ★ 13k • written 9.5 years ago by ▴ 10
1
vote
5
replies
8.2k
views
is it possible to use TPM in DESeq2 ?
counts Normalization DESeq2
updated 23 months ago by ★ 1.3k • written 23 months ago by ▴ 10
0
votes
5
replies
6.4k
views
unable to find an inherited method for function counts for signature DESeqTransform
deseq2 counts DESeqtransform variance deviation
updated 6.5 years ago by 41k • written 6.5 years ago by • 0
1
vote
1
reply
5.7k
views
Not full rank design using Deseq2
deseq2 design counts
updated 9.2 years ago by 41k • written 9.2 years ago by ▴ 30
4
votes
4
replies
4.9k
views
FeatureCounts
counts subread RNASeq featurecounts
2.5 years ago k___ ▴ 30
2
votes
4
replies
4.6k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
5.0 years ago • updated 4.1 years ago Mozart ▴ 30
2
votes
1
reply
3.9k
views
DESeq2 Input format
deseq2 counts
updated 7.6 years ago by 41k • written 7.6 years ago by • 0
2
votes
3
replies
3.7k
views
Deseq2: padj value changes with varying alpha
deseq2 counts rnaseq
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 10
1
vote
3
replies
3.3k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools deseq2 counts cuffdiff
8.2 years ago Jon Bråte ▴ 250
0
votes
3
replies
3.3k
views
Handling pseudogenes in RNA-seq
rna-seq pseudogenes STAR counts
updated 5.9 years ago by ★ 1.1k • written 5.9 years ago by • 0
6
votes
4
replies
3.2k
views
Can edgeR TMM normalization be used for other count data?
edgeR tmm normalization counts
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 40
0
votes
2
replies
3.1k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 3.5 years ago by 41k • written 3.5 years ago by • 0
2
votes
5
replies
3.0k
views
Limma/DESeq2: Statistic and readcount of biological replicates
normalization limma deseq2 counts
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 90
2
votes
4
replies
2.5k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
8.3 years ago bioprog • 0
2
votes
3
replies
2.3k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 3.0 years ago by ★ 5.2k • written 6.0 years ago by ▴ 10
0
votes
7
replies
2.3k
views
Count filter for differential expression
edger limma counts
updated 5.4 years ago by 50k • written 5.4 years ago by • 0
2
votes
4
replies
1.9k
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 5.6 years ago by 50k • written 5.6 years ago by • 0
2
votes
2
replies
1.9k
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 7.9 years ago by 41k • written 7.9 years ago by • 0
1
vote
8
replies
1.9k
views
[Outlier Gene removal] - One sample with outlier counts for some genes
RNAseq DESeq2 outlier counts DE analysis
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by • 0
1
vote
5
replies
1.8k
views
deseq2 normalized data
regression deseq2 counts
updated 8.6 years ago by 41k • written 8.6 years ago by • 0
4
votes
2
replies
1.8k
views
Help: extract counts from RNA-seq .bam/.bai files
counts edger
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 70
0
votes
3
replies
1.5k
views
DESeq2 ComputeSumFactors extract normalized counts
deseq2 normalization counts
updated 6.6 years ago by 41k • written 6.6 years ago by • 0
0
votes
1
reply
1.5k
views
IRanges object from count matrix
genomicranges iranges featurecounts counts rnaseq
updated 7.2 years ago by 16k • written 7.2 years ago by ★ 1.5k
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 23 months ago by ★ 1.3k • written 23 months ago by ▴ 10
0
votes
1
reply
1.4k
views
DEXSeq error: Count files do not correspond to the flattened annotation file
DEXSeq counts gff
9.5 years ago Assa Yeroslaviz ★ 1.5k
3
votes
1
reply
1.4k
views
log2 of normalized counts for further analyzes
DESeq2 log2 normalized counts
updated 14 months ago by 65k • written 14 months ago by ▴ 10
0
votes
7
replies
1.4k
views
Results table completely wrong for specified contrast of
DESeq2 logfoldchange counts
updated 5.3 years ago by 41k • written 5.3 years ago by ▴ 40
1
vote
3
replies
1.4k
views
DESeq2: Do basemean values take into account interaction effects?
deseq2 counts normalized counts
updated 7.7 years ago by ★ 13k • written 7.7 years ago by ▴ 40
3
votes
1
reply
1.4k
views
window counts in csaw
csaw counts
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
1
vote
4
replies
1.4k
views
comparing transcripts expression between conditions
salmon transcripts significance counts
7.8 years ago Assa Yeroslaviz ★ 1.5k
2
votes
5
replies
1.3k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 9 weeks ago by 41k • written 16 months ago by • 0
5
votes
3
replies
1.3k
views
Combining counts from non-replicate samples in RNA-Seq analysis for a synergistic system
edger normalization counts RNA-seq
updated 4.8 years ago by ★ 28k • written 4.9 years ago by • 0
2
votes
1
reply
1.3k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.1 years ago by ★ 5.2k • written 5.1 years ago by ▴ 10
1
vote
2
replies
1.2k
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 5.6 years ago by 50k • written 5.6 years ago by • 0
0
votes
2
replies
1.2k
views
small RNAs quantification
smallrna counts
7.6 years ago ribioinfo ▴ 100
0
votes
3
replies
972
views
dealing with outliers (deseq2)
maxcooks outliers zero counts DESeq2
updated 2.1 years ago by 41k • written 2.1 years ago by ▴ 10
1
vote
1
reply
953
views
How to compare RNA-seq counts matrices from different aligners ?
rnaseq counts alignement
6.1 years ago Aurora ▴ 20
0
votes
1
reply
921
views
small RNA counts
counts SmallRNA Normalization
updated 2.4 years ago by ▴ 80 • written 2.5 years ago by ▴ 30
0
votes
0
replies
900
views
Combined strand specific and unstranded samples
strand rnaseq differential gene expression batch effect counts
6.6 years ago lirongrossmann ▴ 80
0
votes
0
replies
697
views
using gene expression matrix for TCseq package to cluster genes
TCseq microwarray cluster counts normalization
4.7 years ago bioyas ▴ 10
43 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Awards • All
Popular Question to James W. MacDonald 65k
Scholar to Michael Love 41k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Locations • All
France, 3 minutes ago
United States, 15 minutes ago
Sweden, 18 minutes ago
United States, 19 minutes ago
The Netherlands, 27 minutes ago
Traffic: 1119 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6