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33
votes
16
replies
35k
views
Differential expression analysis starting from TPM data
R TPM
updated 6.2 years ago by 48k • written 6.2 years ago by ▴ 90
24
votes
6
replies
34k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 18 months ago by ▴ 20 • written 6.7 years ago by ▴ 50
22
votes
14
replies
5.8k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 16 months ago by • 0 • written 17 months ago by ▴ 50
16
votes
14
replies
34k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 15 months ago by • 0 • written 6.2 years ago by ▴ 20
10
votes
13
replies
3.9k
views
Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
R limma oligo differential gene expression affymetrix microarrays
updated 8.2 years ago by • 0 • written 8.2 years ago by ▴ 10
10
votes
8
replies
2.2k
views
Best alternative annotation package to BiomaRt
R biomaRt Ensembl rnaseq
4.2 years ago m93 ▴ 10
9
votes
7
replies
3.6k
views
WGCNA: relate modules to binary trait
WGCNA module eigengene binary trait R
updated 4.7 years ago by ▴ 30 • written 4.7 years ago by ▴ 50
9
votes
8
replies
20k
views
Integrating DESeq2 and TopGO for Enrichment
go deseq2 rnaseq r
updated 8.6 years ago by ▴ 610 • written 8.6 years ago by ▴ 20
9
votes
6
replies
2.4k
views
Any method can coerce "list" object to GRanges [reproducible example is included]?
granges error handling R
updated 7.5 years ago by 11k • written 7.5 years ago by ▴ 80
8
votes
11
replies
1.6k
views
Creating design matrix in LIMMA
limma microarray R
6.7 years ago sgblackpearl • 0
8
votes
4
replies
997
views
maintainer option for bioconductor packages
bioconductor R
updated 4.9 years ago by 63k • written 4.9 years ago by ▴ 70
8
votes
9
replies
5.6k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 8.2 years ago by • 0 • written 8.2 years ago by ★ 1.5k
8
votes
11
replies
9.7k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5 r hdf5
updated 5 months ago by • 0 • written 6.3 years ago by ▴ 10
8
votes
5
replies
2.8k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 4.4 years ago by 48k • written 4.4 years ago by ▴ 110
7
votes
4
replies
4.8k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 10 months ago by ▴ 10 • written 17 months ago by ▴ 40
7
votes
13
replies
1.8k
views
Test whether expression levels of two gene sets are significantly different
R DESeq2 gene set testing gene expression
6.9 years ago Jon Bråte ▴ 250
7
votes
7
replies
1.3k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 4.9 years ago by 21k • written 4.9 years ago by ▴ 50
7
votes
6
replies
2.7k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2 R RNASeqR
2.8 years ago ecg1g15 ▴ 20
7
votes
3
replies
3.6k
views
VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
r limma voom vsn
updated 10 months ago by 48k • written 4.6 years ago by ▴ 70
7
votes
15
replies
3.2k
views
Differentially expressed genes selection with FC and FDR cutoff
edgeR rnaseq r bioconductor
updated 5.3 years ago by 48k • written 5.3 years ago by ▴ 50
7
votes
8
replies
1.2k
views
Where downloaded data are stored?
R
8.4 years ago Arman Shahrisa ▴ 20
7
votes
13
replies
2.0k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 3.5 years ago by ★ 3.0k • written 3.5 years ago by ▴ 110
7
votes
9
replies
2.8k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 8 months ago by ★ 2.8k • written 4.4 years ago by ▴ 10
7
votes
9
replies
1.5k
views
codelink package is not installing
codelink r
8.4 years ago Agaz Hussain Wani ▴ 260
7
votes
13
replies
2.8k
views
Finding the coordinates from a BCV plot in edgeR
r edgeR estimatedispersions coordinate
7.8 years ago pertille • 0
7
votes
1
reply
1.4k
views
What is the best way to get help on Bioconductor packages?
Bioconductor R Suggestion
updated 8.3 years ago by ★ 8.2k • written 8.3 years ago by ▴ 10
7
votes
5
replies
2.7k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
2.8 years ago ecg1g15 ▴ 20
6
votes
4
replies
2.6k
views
deseq2 estimating size factors
r deseq2
updated 7.5 years ago by 40k • written 7.5 years ago by ▴ 40
6
votes
11
replies
6.7k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges split r
updated 21 months ago by ▴ 40 • written 7.7 years ago by ▴ 80
6
votes
3
replies
2.7k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 10
6
votes
7
replies
2.1k
views
Differences between RTCGA and TCGAbiolinks data
r survival analysis rtcga tcgabiolinks mirna-seq
5.3 years ago atakanekiz ▴ 30
6
votes
3
replies
6.7k
views
Heatmap Plotting in R
heatmap R bioconductor
8.2 years ago • updated 6.5 years ago Deepak Tanwar ▴ 10
6
votes
7
replies
3.6k
views
unexpected error when creating GRanges object by calling makeGRangesFromDataFrame()
r error handling granges
updated 7.6 years ago by 16k • written 7.6 years ago by ▴ 80
6
votes
2
replies
12k
views
DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
deseq2 R rnaseq
updated 7.7 years ago by 40k • written 7.7 years ago by • 0
6
votes
7
replies
1.5k
views
How to implement element-wise-overlaps with iteration for two different bed files in R?
r findoverlaps iterators
updated 7.7 years ago by 16k • written 7.7 years ago by ▴ 80
6
votes
2
replies
1.6k
views
permutation test against intervals
R pkg
updated 8.3 years ago by ▴ 30 • written 8.5 years ago by ▴ 20
6
votes
6
replies
1.6k
views
Can i set a path for readCodlinkSet()
r differential expression codelink
updated 8.3 years ago by ▴ 760 • written 8.3 years ago by ▴ 260
6
votes
10
replies
4.5k
views
defining a function for multiple paired t.test in many rows of a microarray dataset
microarray r t.test bioconductor
updated 8.7 years ago by 48k • written 8.7 years ago by ▴ 810
6
votes
4
replies
1.5k
views
Filtering after a contrast
deseq2 r filtering bioconductor
updated 7.1 years ago by 13k • written 7.1 years ago by • 0
6
votes
11
replies
1.4k
views
"associated_gene" attribute from biomaRt returns too few values - SNP(rsID dataset)
r biomart SNP annotation HUGO
updated 3.1 years ago by ★ 6.1k • written 3.1 years ago by • 0
5
votes
1
reply
3.0k
views
RNAseq analysis: what comes first, filtering or normalization
edger R rnaseq
updated 4.7 years ago by ★ 28k • written 4.8 years ago by ▴ 30
5
votes
10
replies
1.8k
views
caught segfault error when loading S4Vectors package in R
R S4Vectors segfault
updated 4.6 years ago by 25k • written 4.6 years ago by ▴ 20
5
votes
4
replies
4.0k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
6.5 years ago • updated 6.2 years ago salamandra ▴ 20
5
votes
2
replies
1.2k
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
7.2 years ago • updated 6.9 years ago Jurat Shahidin ▴ 80
5
votes
3
replies
1.1k
views
How to avoid repeated overlap pair for GRanges object in grid?
r genomicranges
7.2 years ago • updated 6.9 years ago Jurat Shahidin ▴ 80
5
votes
0
replies
1.3k
views
Job: Summer Studentships in Data Science (Computational Cancer Biology) at the University of Cambridge
R python deep learning machine learning cancer genomics Job
6.5 years ago Shamith.Samarajiwa ▴ 180
5
votes
2
replies
1.6k
views
DESeq2 batch effect with and without interaction model
deseq2 rna-seq R linear model design matrix
updated 5.9 years ago by 40k • written 5.9 years ago by ▴ 10
5
votes
7
replies
1.3k
views
Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
R decipher biostrings
updated 5.7 years ago by ▴ 150 • written 5.7 years ago by • 0
5
votes
22
replies
5.0k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 7.2 years ago by ▴ 990 • written 8.6 years ago by • 0
5
votes
14
replies
4.3k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 7.8 years ago by ★ 8.2k • written 7.8 years ago by ▴ 50
50 results • Page 1 of 1
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Replies
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…
Votes
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Answer: Batch correction and repeated measures
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