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txImportData
•
reset
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
10 months ago
Ndimensional
▴ 20
0
votes
2
replies
669
views
tximport error in reading salmon output files?
tximport
tximportData
updated 3 months ago by
Matteo
• 0 • written 10 months ago by
barrypraveen
• 0
2
votes
3
replies
1.3k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
17 months ago
mohammedtoufiq91
▴ 10
3
votes
3
replies
939
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
18 months ago
duhwa.lee
• 0
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
22 months ago
uhlkatie
• 0
2
votes
3
replies
963
views
Import RSEM output without sample data
DESeq2
tximportData
tximport
updated 2.2 years ago by
Michael Love
42k • written 2.2 years ago by
Luisa
• 0
0
votes
3
replies
923
views
tximport fails when RSEM output options produce files with additional columns?
DESeq2
tximportData
tximpor
updated 2.8 years ago by
Michael Love
42k • written 2.8 years ago by
Alexander
• 0
0
votes
1
reply
848
views
Multi-factor Analysis in DeSEQ2
tximport
R
tximportData
RNASeq
DESeq2
updated 3.0 years ago by
Michael Love
42k • written 3.0 years ago by
pthom010
• 0
0
votes
7
replies
1.7k
views
Problem with Tximport
tximportData
tximport
3.3 years ago
agoesmartini
• 0
0
votes
1
reply
923
views
How to use tx import on output of abundance file
tximportData
tximport
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 years ago by
Julie
• 0
0
votes
4
replies
1.1k
views
Having a hard time creating a Txi object from an existing Salmon output file to convert transcript file to gene id TPM
Salmon
tximport
tximportdata
ensembl
updated 4.1 years ago by
Michael Love
42k • written 4.1 years ago by
slouis
• 0
1
vote
2
replies
1.0k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport
tximportdata
salmon
5.5 years ago
fcuy047
• 0
1
vote
2
replies
1.2k
views
trouble importing data for DEseq2 workflow
deseq2
tximport
tximportdata
pasilla
Tutorial
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
Stanley Yang
• 0
1
vote
8
replies
33k
views
How to create tx2gene.gencode.v27.csv
tximportdata
updated 5.9 years ago by
Michael Love
42k • written 5.9 years ago by
mmokrejs
• 0
2
votes
6
replies
1.6k
views
[DESeq2] Different results from tutorial
deseq2
tximportdata
tximport
updated 6.0 years ago by
Michael Love
42k • written 6.0 years ago by
changhan1110
• 0
0
votes
1
reply
2.4k
views
could not find function "tximport"
tximportdata
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
s.corley
▴ 30
0
votes
3
replies
13k
views
Problem installing tximportData
tximportdata
7.2 years ago
elg
• 0
3
votes
5
replies
2.7k
views
txImport: a gene seems missing from the sample data
txImportData
txImport
updated 3.3 years ago by
James W. MacDonald
65k • written 7.2 years ago by
alexlok
• 0
0
votes
1
reply
1.7k
views
How to remove genes with 0 counts in tximport?
tximport
deseq
tximportdata
deseq2
updated 7.3 years ago by
Michael Love
42k • written 7.3 years ago by
Peter Alto
▴ 10
0
votes
7
replies
1.7k
views
PCA results different from th same sample but different counting method
deseq2
pca
tximportdata
htseqcounts
updated 7.8 years ago by
Michael Love
42k • written 7.8 years ago by
jarod_v6@libero.it
▴ 40
0
votes
9
replies
3.5k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte
tximportData
updated 6.3 years ago by
hauken_heyken
▴ 80 • written 7.9 years ago by
jarod_v6@libero.it
▴ 40
21 results • Page
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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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