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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
3.5k
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
★ 4.0k • 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
1.5k
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
1.9k
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
5.4k
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 7.5 years ago by
Gordon Smyth
50k • written 7.5 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
7.6 years ago
komal.rathi
▴ 120
3
votes
4
replies
2.0k
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 8.7 years ago by
Michael Love
41k • written 8.7 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 9.0 years ago by
Gordon Smyth
50k • written 9.0 years ago by
thibault.lorin
▴ 10
19 results • Page
1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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