Showing : tpm • reset
2
votes
3
replies
1.5k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
2
votes
14
replies
7.5k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 14 months ago by • 0 • written 6.7 years ago by ▴ 110
2
votes
5
replies
11k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq normalization tpm tmm
8.5 years ago nickbern92 • 0
6
votes
8
replies
2.7k
views
Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
RNASeq-quantification edgeR TPM
updated 5.2 years ago by 50k • written 5.2 years ago by ▴ 20
33
votes
16
replies
39k
views
Differential expression analysis starting from TPM data
R TPM
updated 6.7 years ago by 50k • written 6.7 years ago by ▴ 90
32
votes
16
replies
17k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.0 years ago by ▴ 20 • written 7.8 years ago by ▴ 190
2
votes
18
replies
3.4k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
6.1 years ago stephan.emmrich ▴ 10
0
votes
1
reply
1.2k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
2
votes
2
replies
1.2k
views
How to use TPM in plotMA in DESeq2
TPM deseq2
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
2
votes
4
replies
1.4k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
12 months ago vk • 0
0
votes
1
reply
2.1k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2 tpm heatmap pheatmap
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 40
0
votes
1
reply
1.5k
views
Set rnaseq locial flag during GSVA
gsva rnaseq tpm
updated 6.6 years ago by ★ 3.2k • written 6.7 years ago by • 0
1
vote
3
replies
4.4k
views
PCA from TPM
pca tpm tximport
6.5 years ago tanyabioinfo ▴ 20
0
votes
1
reply
2.3k
views
Normalize depth before calculating TPM
rna-seq TPM library size factor
6.4 years ago colore • 0
2
votes
3
replies
1.4k
views
RNA-seq: Time-course data normalisation with TPM
rna-seq normalization deseq2 TPM
updated 6.1 years ago by 41k • written 6.1 years ago by ▴ 10
2
votes
2
replies
1.0k
views
Normalizing 5' Nascent RNA-seq data to identify differentially expressed transcription start sites
DESeq2 tpm Normalization
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
0
votes
2
replies
1.5k
views
DESeq2 Log2 fold change does not make sense given change in TPM
DESeq2 TPM Foldchange
updated 2.0 years ago by 41k • written 2.0 years ago by • 0
0
votes
1
reply
704
views
How to make the data compatible for DESeq2?
DESeq2 TPM rawcounts StringTie
updated 20 months ago by 41k • written 20 months ago by ▴ 20
4
votes
5
replies
2.1k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 20 months ago by 41k • written 20 months ago by ▴ 10
1
vote
4
replies
4.3k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
2.6 years ago Sandhiya • 0
16
votes
25
replies
2.9k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.0 years ago by ▴ 60
5
votes
8
replies
1.7k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 4.5 years ago by ★ 13k • written 4.5 years ago by ▴ 30
2
votes
2
replies
1.5k
views
How to Analyse Datasets from GEO
geo rnaseq deseq2 tpm
updated 3.9 years ago by ★ 3.9k • written 4.0 years ago by ▴ 10
2
votes
2
replies
2.0k
views
tximport counts versus TPM
tximport TPM
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 620
2
votes
1
reply
1.9k
views
ensembl to hgnc symbols creates duplicates
r biomart genemap TPM
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by ▴ 60
1
vote
4
replies
1.0k
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 3.5 years ago by 41k • written 3.6 years ago by • 0
2
votes
3
replies
1.7k
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 3.4 years ago by 50k • written 3.4 years ago by ▴ 90
1
vote
4
replies
1.4k
views
merge TPM values for same geneID
RNASeqRData TPM
updated 18 months ago by ★ 4.0k • written 18 months ago by ▴ 10
0
votes
1
reply
1.5k
views
TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
5.9 years ago Ina Hoeschele ▴ 620
0
votes
2
replies
741
views
multiple correction on mean of TPM
TPM
18 months ago Harish.Sudarsanam • 0
0
votes
0
replies
1.2k
views
ExpressionAtlas: download RPKM/TPM
ExpressionAtlas EMBL TPM
6.3 years ago António Miguel de Jesus Domingues ▴ 490
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
1
vote
3
replies
1.5k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
6.6 years ago lirongrossmann ▴ 80
33 results • Page 1 of 1
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Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
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