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fpkm
•
reset
3
votes
3
replies
1.6k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
10 months ago
Ethan Nguyen
• 0
2
votes
4
replies
1.7k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2
BatchEffect
tpm
fpkm
15 months ago
vk
• 0
0
votes
5
replies
4.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.5 years ago by
ATpoint
★ 4.2k • written 3.3 years ago by
Xiaojie Cheng
• 0
1
vote
4
replies
4.6k
views
Conversion from FPKM,RPKM to tpm
DESEQ2
fpkm
rpkm
tpm
2.8 years ago
Sandhiya
• 0
0
votes
1
reply
1.8k
views
Doing differential expression using FPKM , samples don't have replication
dge
fpkm
rna-seq
updated 3.2 years ago by
Kevin Blighe
★ 4.0k • written 3.2 years ago by
lkianmehr
• 0
1
vote
4
replies
1.1k
views
tximport abundanceCol parameter not functioning for rsem data
tximport
rsem
transcript abundance
TPM
FPKM
updated 3.7 years ago by
Michael Love
42k • written 3.9 years ago by
m.metsger
• 0
2
votes
5
replies
12k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 9 months ago by
Hamza
• 0 • written 5.6 years ago by
chiara.facciotto
• 0
9
votes
5
replies
4.6k
views
Finding DE genes from RNA-seq data
edgeR
pvalue
qvalue
fpkm
differential gene expression
updated 5.8 years ago by
Steve Lianoglou
★ 13k • written 5.8 years ago by
Harrisonesmith
• 0
2
votes
4
replies
2.1k
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 5.8 years ago by
Gordon Smyth
51k • written 5.8 years ago by
ZihaoXing
• 0
1
vote
2
replies
1.3k
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 5.8 years ago by
Gordon Smyth
51k • written 5.8 years ago by
ZihaoXing
• 0
0
votes
1
reply
1.6k
views
TPM and FPKM for lncRNA
GenomicFeatures
TPM
FPKM
lncRNA
6.2 years ago
Ina Hoeschele
▴ 620
4
votes
4
replies
5.6k
views
Best DEG tool for datasets with FPKM counts?
FPKM
6.7 years ago
Nithisha
▴ 10
1
vote
8
replies
3.4k
views
Add avgTxLength to DESeqDataSet
deseq2
fpkm
updated 3.0 years ago by
Michael Love
42k • written 7.0 years ago by
rhart
• 0
1
vote
1
reply
1.3k
views
FPKM normalization questions!
r
fpkm
bioinformatics
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
fromhj304
▴ 10
5
votes
5
replies
3.0k
views
Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
edgeR
logFC
FPKM
updated 7.8 years ago by
Gordon Smyth
51k • written 7.8 years ago by
Sara
▴ 10
5
votes
9
replies
6.1k
views
Voom: need at least two non-NA values to interpolate
limma voom
voom
rsem
fpkm
7.9 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
8.5 years ago
Jon Bråte
▴ 250
2
votes
8
replies
4.5k
views
How to annotate DESeq2 object with gene size to get FPKMs
deseq2
fpkm
updated 9.0 years ago by
Michael Love
42k • written 9.0 years ago by
ashley.doane
▴ 20
7
votes
4
replies
2.6k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count
rnaseq
rpkm
fpkm
edgeR
updated 9.3 years ago by
Gordon Smyth
51k • written 9.3 years ago by
thibault.lorin
▴ 10
19 results • Page
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Lluís Revilla Sancho
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Michael Love
42k
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★ 1.1k
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