Showing : fpkm • reset
3
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3
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Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
19 months ago Ethan Nguyen • 0
2
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4
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2.2k
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
2.0 years ago vk • 0
0
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5
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5.4k
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.3 years ago by ★ 4.8k • written 4.1 years ago by • 0
1
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4
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Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
3.6 years ago Sandhiya • 0
0
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1
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2.6k
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Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by • 0
1
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4
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1.4k
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tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 4.5 years ago by 43k • written 4.6 years ago by • 0
2
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5
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16k
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Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 18 months ago by • 0 • written 6.4 years ago by • 0
9
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5
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6.0k
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Finding DE genes from RNA-seq data
edgeR pvalue qvalue fpkm differential gene expression
updated 6.5 years ago by ★ 13k • written 6.5 years ago by • 0
2
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4
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2.5k
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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 6.6 years ago by 52k • written 6.6 years ago by • 0
1
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2
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1.5k
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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 6.6 years ago by 52k • written 6.6 years ago by • 0
0
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1
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1.8k
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TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
6.9 years ago Ina Hoeschele ▴ 620
4
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4
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6.2k
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Best DEG tool for datasets with FPKM counts?
FPKM
7.5 years ago Nithisha ▴ 10
1
vote
8
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3.8k
views
Add avgTxLength to DESeqDataSet
deseq2 fpkm
updated 3.8 years ago by 43k • written 7.7 years ago by • 0
1
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1
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1.5k
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FPKM normalization questions!
r fpkm bioinformatics
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 10
5
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5
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3.5k
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Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
edgeR logFC FPKM
updated 8.5 years ago by 52k • written 8.5 years ago by ▴ 20
5
votes
9
replies
6.7k
views
Voom: need at least two non-NA values to interpolate
limma voom voom rsem fpkm
8.6 years ago komal.rathi ▴ 120
3
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4
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2.4k
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Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2 cummerbund rlog fpkm clustering
9.3 years ago Jon Bråte ▴ 260
2
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8
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4.9k
views
How to annotate DESeq2 object with gene size to get FPKMs
deseq2 fpkm
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 20
7
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4
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3.0k
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Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count rnaseq rpkm fpkm edgeR
updated 10.0 years ago by 52k • written 10.0 years ago by ▴ 10
19 results • Page 1 of 1
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Replies
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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