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lncRNA
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how to convert lncRNA probe name or mRNA probe name to gene symbol
lncRNA
probeID
mRNA
genesymbol
7 months ago
Sooni
▴ 10
3
votes
3
replies
1.1k
views
Recount data for unannotated genes
recount
RNAseq
gencode
lncRNA
gene annotation
updated 4.4 years ago by
chris.wilks
▴ 70 • written 4.5 years ago by
francesco.gandolfi
▴ 20
0
votes
1
reply
1.3k
views
TPM and FPKM for lncRNA
GenomicFeatures
TPM
FPKM
lncRNA
5.3 years ago
Ina Hoeschele
▴ 620
0
votes
2
replies
2.5k
views
lncRNA annotation for featureCouns and STAR
lncRNA
featureCounts
STAR
annotation
updated 5.3 years ago by
Wei Shi
★ 3.5k • written 5.3 years ago by
inah
▴ 10
0
votes
2
replies
1.1k
views
R packages for differential expression analysis of raw data from arraystar microarrays
microarray
lncrna
microrna
mrna
raw data
updated 5.8 years ago by
Axel Klenk
▴ 990 • written 5.8 years ago by
ntagaras
• 0
0
votes
3
replies
2.8k
views
Annotation DB for ArrayStar lncRNA arrays
arraystar
lncRNA
annotation
annotationdbi
updated 8.1 years ago by
xiangy7
• 0 • written 8.5 years ago by
Kevin Coombes
▴ 430
6 results • Page
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Answer: Batch effect adjust in model matrix
by
ATpoint
★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Christian
• 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Christian
• 0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…
Votes
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Answer: Batch correction and repeated measures
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