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0
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7
replies
1.6k
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Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error
RStudio
ggplot2
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
BioES
• 0
10
votes
10
replies
6.9k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 6 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
0
votes
0
replies
284
views
proActiv - Error in estimateSizeFactorsForMatrix when using the proActiv function
proActiv
error
estimateSizeFactorsForMatrix
6 months ago
Chris
• 0
0
votes
1
reply
407
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
6 months ago
leon
• 0
0
votes
3
replies
631
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config
DiffBind
Error
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
jason.kost
• 0
0
votes
17
replies
3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 10 months ago by
snow34
• 0 • written 6.6 years ago by
ap3637
• 0
0
votes
1
reply
479
views
Calculate RPKMs and Output proteins pass the cutoff into FASTA file ... Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse") : i…
customProDB
easyrun
error
mm10
Mus_musculus_Data
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Esraa
• 0
0
votes
8
replies
1.2k
views
fail to annotate chromosome data to single cell object
error
SingleCell
annotate
updated 5 months ago by
yw24418
• 0 • written 14 months ago by
sandra.garces.19
• 0
8 results • Page
1 of 1
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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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
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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