Showing : rpkm • reset
0
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0
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1.7k
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
18 months ago Gordon Smyth 52k
1
vote
4
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5.4k
views
Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
3.4 years ago Sandhiya • 0
9
votes
10
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8.8k
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How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 23 months ago by ▴ 20 • written 4.4 years ago by ▴ 10
1
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5
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1.8k
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bug in "dispersion" argument in edgeR - rpkmByGroup
edger rpkm
updated 5.7 years ago by • 0 • written 5.7 years ago by • 0
7
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3
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4.1k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 10
2
votes
1
reply
1.7k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 10
1
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1
reply
1.3k
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Generating RPKM data from dds (DESeq2 pipeline)
deseq2 dds RPKM
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
32
votes
16
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20k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.9 years ago by ▴ 20 • written 8.7 years ago by ▴ 200
3
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1
reply
1.4k
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RMS question in MEDIPS
RMS RPKM MEDIPS
updated 7.0 years ago by ▴ 570 • written 7.0 years ago by ▴ 10
2
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14
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8.9k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 2.0 years ago by ▴ 20 • written 7.6 years ago by ▴ 120
3
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2
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1.9k
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AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub roadmap project rpkm data.frame
8.4 years ago wcstcyx ▴ 30
4
votes
2
replies
5.8k
views
How to run the rpkm function of edgeR
edger rpkm
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 20
4
votes
10
replies
5.9k
views
Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm gene length count matrix edgeR rsubread
9.4 years ago AB ▴ 110
4
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1
reply
2.6k
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Get source code for rpkm() function in edgeR
edgeR rpkm source code
updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 10
7
votes
4
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2.9k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count rnaseq rpkm fpkm edgeR
updated 9.9 years ago by 52k • written 9.9 years ago by ▴ 10
3
votes
3
replies
7.6k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 10.0 years ago by ▴ 370 • written 10.0 years ago by • 0
0
votes
5
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2.9k
views
count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq edger rpkm
updated 10.0 years ago by ▴ 320 • written 10.0 years ago by ▴ 80
4
votes
4
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22k
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edgeR rpkm function
edger rpkm
updated 23 months ago by 52k • written 10.1 years ago by ▴ 30
3
votes
2
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17k
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how to calculate gene length to be used in rpkm() in edgeR
RNASeq edgeR rpkm
updated 22 months ago by 52k • written 10.8 years ago by ★ 1.0k
2
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1
reply
1.8k
views
Shoud I use "aligned reads" or total reads (aligned + unassigned) to the RPKM value?
rnaseq R rsubread rpkm
updated 10.4 years ago by 68k • written 10.4 years ago by • 0
20 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
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A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
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