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FPKM
•
reset
3
votes
3
replies
430
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
14 days ago
Ethan Nguyen
• 0
2
votes
4
replies
637
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2
BatchEffect
tpm
fpkm
5 months ago
vk
• 0
0
votes
5
replies
2.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 20 months ago by
ATpoint
★ 3.4k • written 2.5 years ago by
Xiaojie Cheng
• 0
1
vote
4
replies
3.5k
views
Conversion from FPKM,RPKM to tpm
DESEQ2
fpkm
rpkm
tpm
2.0 years ago
Sandhiya
• 0
0
votes
1
reply
1.0k
views
Doing differential expression using FPKM , samples don't have replication
dge
fpkm
rna-seq
updated 2.3 years ago by
Kevin Blighe
3.8k • written 2.3 years ago by
lkianmehr
• 0
1
vote
4
replies
810
views
tximport abundanceCol parameter not functioning for rsem data
tximport
rsem
transcript abundance
TPM
FPKM
updated 2.9 years ago by
Michael Love
40k • written 3.0 years ago by
m.metsger
• 0
2
votes
4
replies
8.9k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 4.5 years ago by
Ahmed Alhendi
• 0 • written 4.8 years ago by
chiara.facciotto
• 0
9
votes
5
replies
3.6k
views
Finding DE genes from RNA-seq data
edgeR
pvalue
qvalue
fpkm
differential gene expression
updated 4.9 years ago by
Steve Lianoglou
13k • written 4.9 years ago by
Harrisonesmith
• 0
2
votes
4
replies
1.5k
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 5.0 years ago by
Gordon Smyth
48k • written 5.0 years ago by
ZihaoXing
• 0
1
vote
2
replies
994
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 5.0 years ago by
Gordon Smyth
48k • written 5.0 years ago by
ZihaoXing
• 0
0
votes
1
reply
1.3k
views
TPM and FPKM for lncRNA
GenomicFeatures
TPM
FPKM
lncRNA
5.3 years ago
Ina Hoeschele
▴ 620
4
votes
4
replies
4.8k
views
Best DEG tool for datasets with FPKM counts?
FPKM
5.9 years ago
Nithisha
▴ 10
1
vote
8
replies
2.8k
views
Add avgTxLength to DESeqDataSet
deseq2
fpkm
updated 2.2 years ago by
Michael Love
40k • written 6.2 years ago by
rhart
• 0
1
vote
1
reply
1.1k
views
FPKM normalization questions!
r
fpkm
bioinformatics
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
fromhj304
▴ 10
5
votes
5
replies
2.6k
views
Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
edgeR
logFC
FPKM
updated 7.0 years ago by
Gordon Smyth
48k • written 7.0 years ago by
Sara
▴ 10
5
votes
9
replies
5.5k
views
Voom: need at least two non-NA values to interpolate
limma voom
voom
rsem
fpkm
7.1 years ago
komal.rathi
▴ 110
3
votes
4
replies
1.8k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2
cummerbund
rlog
fpkm
clustering
7.7 years ago
Jon Bråte
▴ 250
2
votes
8
replies
3.9k
views
How to annotate DESeq2 object with gene size to get FPKMs
deseq2
fpkm
updated 8.2 years ago by
Michael Love
40k • written 8.2 years ago by
ashley.doane
▴ 20
7
votes
4
replies
2.2k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count
rnaseq
rpkm
fpkm
edgeR
updated 8.5 years ago by
Gordon Smyth
48k • written 8.5 years ago by
thibault.lorin
▴ 10
19 results • Page
1 of 1
Recent ...
Replies
Comment: Exporting DESeq2 filtered results
by
James W. MacDonald
63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block()
by
Hervé Pagès
16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block()
by
Hervé Pagès
16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Comment: Biostrings error at retrieving protein sequences
by
Hervé Pagès
16k
Yes, but you need to put the clean names back on the AAStringSet object: ``` names(protein_sequences) <- gsub(" .*", "", names(protein_sequ…
Comment: Exporting DESeq2 filtered results
by
camillab.
▴ 10
thanks! I didn't`t notice that. I will cancel it now!
Votes
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
A: Effect of lfcThreshold on p-value in DESeq2
Comment: Mixed up sample info with plotPCA
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Gordon Smyth
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James W. MacDonald
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