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quality
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First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq
PCA
control
DESeq2
Quality
2.2 years ago • updated 2.0 years ago
9906201a
▴ 20
0
votes
0
replies
610
views
AffyExpress choose relative path folder
folder
quality
QualityControl
AffyExpress
3.4 years ago
bastien_chassagnol
• 0
0
votes
3
replies
2.2k
views
what does "mean base quality" mean?
base quality
quality
mean base quality
updated 7.6 years ago by
Mike Smith
★ 6.5k • written 7.6 years ago by
christiangriffioen
• 0
0
votes
1
reply
853
views
Array quality metrics for large sample size
microarray
quality
updated 5.3 years ago by
Wolfgang Huber
★ 13k • written 5.3 years ago by
RV
▴ 10
4 results • Page
1 of 1
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga
by
ATpoint
★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Answer: fgsea significant result
by
ATpoint
★ 4.1k
Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient. See https://support.bioconductor.o…
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 …
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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