Showing : CPM • reset
15
votes
6
replies
29k
views
How does edgeR cpm function calculate log(CPM) values?
edgeR cpm
updated 5.9 years ago by ▴ 20 • written 6.1 years ago by ▴ 40
13
votes
3
replies
3.5k
views
EdgeR cpm: factor of 2 when adjusting library size?
edger cpm
8.4 years ago mikaelhc ▴ 20
6
votes
2
replies
2.8k
views
edgeR cpm() function with and without log2
edger cpm
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 360
6
votes
14
replies
2.9k
views
Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
rnaseq analysis variancestabilizingtransformation normalization cpm edger
updated 6.0 years ago by ★ 13k • written 6.0 years ago by ▴ 830
5
votes
4
replies
7.5k
views
edgeR cpm filter with >1 factor
edger cpm multiple factor design independent filtering
8.3 years ago dietahanson ▴ 30
5
votes
6
replies
1.7k
views
How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM filterByExpr edgeR histogram rowsums
17 months ago mohammedtoufiq91 ▴ 10
5
votes
7
replies
2.6k
views
logCPM to CPM conversion after removeBatchEffect()
edger removeBatchEffect cpm logCPM limma
4.9 years ago altintas.ali • 0
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 11 months ago by 50k • written 11 months ago by ▴ 10
5
votes
3
replies
1.7k
views
Support for offsets in cpm and voom functions?
edgeR cpm voom limma
8.6 years ago Ryan C. Thompson ★ 7.9k
4
votes
5
replies
1.1k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
4.2 years ago svlachavas ▴ 830
4
votes
11
replies
4.6k
views
edgeR cpm filter
edger independent filtering multiple factor design cpm
updated 6.5 years ago by 50k • written 6.5 years ago by • 0
3
votes
8
replies
1.4k
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT CPM lowcountgenes deseq2
6.2 years ago A ▴ 40
3
votes
9
replies
1.7k
views
edgeR long vectors support when normalizing abundance matrix
edger cpm
6.6 years ago jtremblay514 • 0
3
votes
2
replies
869
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind CPM TMM
updated 4.1 years ago by ★ 5.2k • written 4.1 years ago by ▴ 40
3
votes
9
replies
1.8k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
13 months ago mohammedtoufiq91 ▴ 10
3
votes
2
replies
994
views
How to calculate average log2 CPM with batch effect?
edger limma cpm
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 360
2
votes
4
replies
1.3k
views
Implementation of specific cpm filtering in RNA-Seq data described in a previously published edgeR pipeline
edger cpm non-specific filtering rnaseq
updated 5.8 years ago by 50k • written 5.8 years ago by ▴ 830
2
votes
7
replies
5.3k
views
Gene Expression Matrix (CPM)
cpm gene expression matrix tmm normailzation
7.2 years ago kkadzi25 • 0
2
votes
7
replies
2.4k
views
About differentially expressed genes that found by edgeR
edgeR DE analysis fold change cpm
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by ▴ 10
2
votes
7
replies
1.6k
views
CPM after RUVseq
RUVSeq CPM Normalization
23 months ago Jess • 0
1
vote
2
replies
2.1k
views
edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
edger filtering cpm
updated 7.7 years ago by 50k • written 7.7 years ago by • 0
1
vote
2
replies
806
views
Should the rlog normalised gene expression counts be further normalised?
rlog CPM RKPM
updated 4.4 years ago by ★ 13k • written 4.4 years ago by ▴ 10
1
vote
1
reply
943
views
Degust: what normalization method does it use
DEGUST Normalization CPM
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
1
vote
6
replies
1.7k
views
extracting cpm expression from limma fit
limma cpm
updated 7.9 years ago by ▴ 10 • written 8.2 years ago by ▴ 40
1
vote
3
replies
2.3k
views
DESeq normalization seems to reverse the directionality of log2FoldChange - is this normal?
deseq2 rnaseq rna-seq normalization cpm
updated 8.0 years ago by ★ 13k • written 8.0 years ago by • 0
0
votes
3
replies
3.5k
views
CPM output from edgeR for a downstream application
CPM edgeR
8.9 years ago ycding ▴ 10
0
votes
3
replies
650
views
Normalization of RNA seq data
RNA seq cpm
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by • 0
0
votes
2
replies
3.3k
views
CPM function in EDGER
edger cpm rnaseq
3.7 years ago francesca3 • 0
0
votes
3
replies
1.2k
views
edgeR:fitted and partial expression values
edgeR cpm edger fitted model explained variance
updated 6.3 years ago by 50k • written 6.3 years ago by ▴ 130
29 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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