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TPM
•
reset
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
2
votes
18
replies
3.5k
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
33
votes
16
replies
39k
views
Differential expression analysis starting from TPM data
R
TPM
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
cahidora
▴ 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
luxeredias
▴ 20 • written 7.8 years ago by
tangming2005
▴ 190
2
votes
14
replies
7.5k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 14 months ago by
Chris
• 0 • written 6.7 years ago by
Biologist
▴ 110
5
votes
8
replies
1.8k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R
limma
TPM
rnaseq
differential expression
updated 4.6 years ago by
Steve Lianoglou
★ 13k • written 4.6 years ago by
atakanekiz
▴ 30
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
Gordon Smyth
50k • written 5.2 years ago by
raf4
▴ 20
2
votes
5
replies
11k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq
normalization
tpm
tmm
8.6 years ago
nickbern92
• 0
4
votes
5
replies
2.2k
views
Which is the best type of data for correlation or survival analysis
TPM
RNASeq
RSEM
DESeq2
updated 20 months ago by
Michael Love
41k • written 20 months ago by
Yang Shi
▴ 10
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
Michael Love
41k • written 3.6 years ago by
m.metsger
• 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
1
vote
4
replies
4.3k
views
Conversion from FPKM,RPKM to tpm
DESEQ2
fpkm
rpkm
tpm
2.6 years ago
Sandhiya
• 0
1
vote
4
replies
1.4k
views
merge TPM values for same geneID
RNASeqRData
TPM
updated 19 months ago by
ATpoint
★ 4.0k • written 19 months ago by
prashali.bansal
▴ 10
1
vote
3
replies
4.5k
views
PCA from TPM
pca
tpm
tximport
6.5 years ago
tanyabioinfo
▴ 20
2
votes
3
replies
1.5k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
gingergeiger22
• 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
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
Michael Love
41k • written 6.1 years ago by
heikki.sarin
▴ 10
2
votes
3
replies
1.7k
views
Normalization for within-sample gene correlation
edgeR
Normalization
DESeq2
tpm
RNASeq
updated 3.4 years ago by
Gordon Smyth
50k • written 3.4 years ago by
tcalvo
▴ 90
2
votes
2
replies
1.5k
views
How to Analyse Datasets from GEO
geo
rnaseq
deseq2
tpm
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
andrej.stoll.de
▴ 10
2
votes
2
replies
2.1k
views
tximport counts versus TPM
tximport
TPM
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
Ina Hoeschele
▴ 620
2
votes
2
replies
1.2k
views
How to use TPM in plotMA in DESeq2
TPM
deseq2
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
georgewwp
• 0
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
Michael Love
41k • written 2.7 years ago by
Carlos
• 0
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
Michael Love
41k • written 3.5 years ago by
m93
• 0
0
votes
2
replies
746
views
multiple correction on mean of TPM
TPM
18 months ago
Harish.Sudarsanam
• 0
0
votes
2
replies
1.6k
views
DESeq2 Log2 fold change does not make sense given change in TPM
DESeq2
TPM
Foldchange
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
dadca596
• 0
0
votes
1
reply
2.3k
views
Normalize depth before calculating TPM
rna-seq
TPM
library size factor
6.4 years ago
colore
• 0
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
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
Michael Love
41k • written 5.5 years ago by
leo_CD
• 0
0
votes
1
reply
1.5k
views
Set rnaseq locial flag during GSVA
gsva
rnaseq
tpm
updated 6.6 years ago by
Robert Castelo
★ 3.3k • written 6.7 years ago by
leiendeckerlu
• 0
0
votes
1
reply
2.1k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2
tpm
heatmap
pheatmap
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
jarod_v6@libero.it
▴ 40
2
votes
1
reply
1.9k
views
ensembl to hgnc symbols creates duplicates
r
biomart
genemap
TPM
updated 3.7 years ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
Matan G.
▴ 60
0
votes
1
reply
715
views
How to make the data compatible for DESeq2?
DESeq2
TPM
rawcounts
StringTie
updated 20 months ago by
Michael Love
41k • written 20 months ago by
snijesh
▴ 20
0
votes
0
replies
1.2k
views
ExpressionAtlas: download RPKM/TPM
ExpressionAtlas
EMBL
TPM
6.4 years ago
António Miguel de Jesus Domingues
▴ 490
33 results • Page
1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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