Showing : FPKM • reset
3
votes
3
replies
2.6k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
16 months ago Ethan Nguyen • 0
2
votes
4
replies
2.1k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
22 months ago • updated 21 months ago vk • 0
0
votes
5
replies
4.8k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.1 years ago by ★ 4.6k • written 3.9 years ago by • 0
1
vote
4
replies
5.3k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
3.4 years ago Sandhiya • 0
0
votes
1
reply
2.4k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
1
vote
4
replies
1.4k
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 4.3 years ago by 43k • written 4.4 years ago by • 0
2
votes
5
replies
14k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 15 months ago by • 0 • written 6.2 years ago by • 0
9
votes
5
replies
5.3k
views
Finding DE genes from RNA-seq data
edgeR pvalue qvalue fpkm differential gene expression
updated 6.3 years ago by ★ 13k • written 6.3 years ago by • 0
2
votes
4
replies
2.4k
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 6.4 years ago by 52k • written 6.4 years ago by • 0
1
vote
2
replies
1.4k
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 6.4 years ago by 52k • written 6.4 years ago by • 0
0
votes
1
reply
1.7k
views
TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
6.7 years ago Ina Hoeschele ▴ 620
4
votes
4
replies
6.0k
views
Best DEG tool for datasets with FPKM counts?
FPKM
7.3 years ago Nithisha ▴ 10
1
vote
8
replies
3.7k
views
Add avgTxLength to DESeqDataSet
deseq2 fpkm
updated 3.6 years ago by 43k • written 7.5 years ago by • 0
1
vote
1
reply
1.4k
views
FPKM normalization questions!
r fpkm bioinformatics
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 10
5
votes
5
replies
3.3k
views
Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
edgeR logFC FPKM
updated 8.3 years ago by 52k • written 8.3 years ago by ▴ 20
5
votes
9
replies
6.5k
views
Voom: need at least two non-NA values to interpolate
limma voom voom rsem fpkm
8.4 years ago komal.rathi ▴ 120
3
votes
4
replies
2.3k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2 cummerbund rlog fpkm clustering
9.1 years ago Jon Bråte ▴ 260
2
votes
8
replies
4.8k
views
How to annotate DESeq2 object with gene size to get FPKMs
deseq2 fpkm
updated 9.5 years ago by 43k • written 9.5 years ago by ▴ 20
7
votes
4
replies
2.9k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count rnaseq rpkm fpkm edgeR
updated 9.8 years ago by 52k • written 9.8 years ago by ▴ 10
19 results • Page 1 of 1
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Replies
Answer: Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes by a.alkema • 0
Oh, that's silly - thanks, will do!
Answer: Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes by James W. MacDonald 67k
This support site is meant to provide support for Bioconductor packages, but `Meffil` is not part of Bioconductor. You could presumably con…
Comment: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
> It looks like the ssgseaParam function might not be passing the > correct parameters to GSVA::gsva() Apparently because of the extra com…
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu by franknappi14 • 0
I tried it and it's working properly.
Answer: accounting for vs. removing batch effects with DESeq2 in RNAseq analysis by ATpoint ★ 4.6k
The vignette covers batch effects as per the authors best practice, please read it and consider following it.
Votes
Comment: Unused arguments error without used arguments in GSVA?
Answer: Reducing and aggregating GRanges with gaps using plyranges
Answer: Find exact GRanges match keeping metadata columns
Answer: Find exact GRanges match keeping metadata columns
Answer: Unused arguments error without used arguments in GSVA?
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