Showing : fpkm • reset
3
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3
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3.4k
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Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
2.1 years ago Ethan Nguyen • 0
2
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4
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2.5k
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
2.5 years ago vk • 0
0
votes
5
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5.9k
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.7 years ago by ★ 5.0k • written 4.6 years ago by • 0
1
vote
4
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5.9k
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Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
4.0 years ago Sandhiya • 0
0
votes
1
reply
2.9k
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Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
1
vote
4
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1.5k
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 4.9 years ago by 43k • written 5.1 years ago by • 0
2
votes
5
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17k
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Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 24 months ago by • 0 • written 6.8 years ago by • 0
9
votes
5
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6.5k
views
Finding DE genes from RNA-seq data
edgeR pvalue qvalue fpkm differential gene expression
updated 7.0 years ago by ★ 13k • written 7.0 years ago by • 0
2
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4
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2.7k
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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 7.1 years ago by 53k • written 7.1 years ago by • 0
1
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2
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1.6k
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 7.1 years ago by 53k • written 7.1 years ago by • 0
0
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1
reply
2.0k
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TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
7.4 years ago Ina Hoeschele ▴ 620
4
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4
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6.4k
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Best DEG tool for datasets with FPKM counts?
FPKM
7.9 years ago Nithisha ▴ 10
1
vote
8
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4.0k
views
Add avgTxLength to DESeqDataSet
deseq2 fpkm
updated 4.2 years ago by 43k • written 8.2 years ago by • 0
1
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1
reply
1.6k
views
FPKM normalization questions!
r fpkm bioinformatics
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 10
5
votes
5
replies
3.6k
views
Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
edgeR logFC FPKM
updated 9.0 years ago by 53k • written 9.0 years ago by ▴ 20
5
votes
9
replies
6.9k
views
Voom: need at least two non-NA values to interpolate
limma voom voom rsem fpkm
9.1 years ago komal.rathi ▴ 120
3
votes
4
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2.5k
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Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2 cummerbund rlog fpkm clustering
9.7 years ago Jon Bråte ▴ 270
2
votes
8
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5.1k
views
How to annotate DESeq2 object with gene size to get FPKMs
deseq2 fpkm
updated 10.2 years ago by 43k • written 10.2 years ago by ▴ 20
7
votes
4
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3.2k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count rnaseq rpkm fpkm edgeR
updated 10.5 years ago by 53k • written 10.5 years ago by ▴ 10
19 results • Page 1 of 1
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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