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fpkm
•
reset
3
votes
3
replies
1.2k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
7 months ago
Ethan Nguyen
• 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
5
replies
3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.3 years ago by
ATpoint
★ 4.1k • written 3.1 years ago by
Xiaojie Cheng
• 0
1
vote
4
replies
4.3k
views
Conversion from FPKM,RPKM to tpm
DESEQ2
fpkm
rpkm
tpm
2.6 years ago
Sandhiya
• 0
0
votes
1
reply
1.6k
views
Doing differential expression using FPKM , samples don't have replication
dge
fpkm
rna-seq
updated 2.9 years ago by
Kevin Blighe
★ 3.9k • written 2.9 years ago by
lkianmehr
• 0
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
5
replies
11k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 6 months ago by
Hamza
• 0 • written 5.4 years ago by
chiara.facciotto
• 0
9
votes
5
replies
4.2k
views
Finding DE genes from RNA-seq data
edgeR
pvalue
qvalue
fpkm
differential gene expression
updated 5.5 years ago by
Steve Lianoglou
★ 13k • written 5.5 years ago by
Harrisonesmith
• 0
2
votes
4
replies
2.0k
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
Gordon Smyth
50k • written 5.6 years ago by
ZihaoXing
• 0
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
Gordon Smyth
50k • written 5.6 years ago by
ZihaoXing
• 0
0
votes
1
reply
1.5k
views
TPM and FPKM for lncRNA
GenomicFeatures
TPM
FPKM
lncRNA
5.9 years ago
Ina Hoeschele
▴ 620
4
votes
4
replies
5.5k
views
Best DEG tool for datasets with FPKM counts?
FPKM
6.5 years ago
Nithisha
▴ 10
1
vote
8
replies
3.2k
views
Add avgTxLength to DESeqDataSet
deseq2
fpkm
updated 2.8 years ago by
Michael Love
41k • written 6.7 years ago by
rhart
• 0
1
vote
1
reply
1.2k
views
FPKM normalization questions!
r
fpkm
bioinformatics
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
fromhj304
▴ 10
5
votes
5
replies
2.9k
views
Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
edgeR
logFC
FPKM
updated 7.6 years ago by
Gordon Smyth
50k • written 7.6 years ago by
Sara
▴ 10
5
votes
9
replies
5.9k
views
Voom: need at least two non-NA values to interpolate
limma voom
voom
rsem
fpkm
7.7 years ago • updated 7.6 years ago
komal.rathi
▴ 120
3
votes
4
replies
2.1k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2
cummerbund
rlog
fpkm
clustering
8.3 years ago
Jon Bråte
▴ 250
2
votes
8
replies
4.3k
views
How to annotate DESeq2 object with gene size to get FPKMs
deseq2
fpkm
updated 8.8 years ago by
Michael Love
41k • written 8.8 years ago by
ashley.doane
▴ 20
7
votes
4
replies
2.5k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count
rnaseq
rpkm
fpkm
edgeR
updated 9.1 years ago by
Gordon Smyth
50k • written 9.1 years ago by
thibault.lorin
▴ 10
19 results • Page
1 of 1
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Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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