User: ATpoint

gravatar for ATpoint
ATpoint30
Reputation:
30
Status:
New User
Location:
Germany
Website:
https://www.biostars.o...
Last seen:
3 days, 15 hours ago
Joined:
2 years, 2 months ago
Email:
a*********@gmail.com

Wet-lab biologist by training, wannaba computational biologist.

Biostars Mod: ATpoint

Posts by ATpoint

<prev • 27 results • page 1 of 3 • next >
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Answer: C: Paired t-test with DESeq2
... Others might give you a statistically-sound response but if you do not have access to the code or any details beyond doing `a t-test on your data` I would not use these results at all. Imagine a reviewer asks you at some point to clarify about the analysis strategy, what would you respond? Maybe you ...
written 5 days ago by ATpoint30
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Comment: C: How to find sites with H3K27me3 loss?
... Cross-posted: https://www.biostars.org/p/398094/ ...
written 4 weeks ago by ATpoint30
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68
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Comment: C: Deseq2 post functional annotation for metagenome
... Cross-posted https://www.biostars.org/p/397969/ ...
written 4 weeks ago by ATpoint30
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Comment: C: Merging two files based on the identifier column (gene symbols)?
... Please do not cross-post. https://www.biostars.org/p/397989/ ...
written 4 weeks ago by ATpoint30
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90
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Comment: C: DESeq2 unpaired RNAseq analysis
... Cross: https://www.biostars.org/p/397399/ ...
written 5 weeks ago by ATpoint30
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1
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67
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1
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Correct use of TMM / normalization factors based on large bins
... The `csaw` package suggests to use TMM normalization based on large, e.g. 10kb, bins across the genome if ChIP-seq samples are expected to show rather global differences / composition bias is expected. As I want to use the resulting normalization factors to scale non-standard (=non `DGElist` files, ...
csaw tmm written 6 weeks ago by ATpoint30
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Comment: C: Problem in featureCounts file.
... Cross-posted: https://www.biostars.org/p/392402/ ...
written 10 weeks ago by ATpoint30
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Comment: C: Paired samples in cell lines using deseq2
... Your samples notably cluster by cell line, not by treatment. Therefore it appears unfortunate to use them as biological replicates. From a biological standpoint this quite normal for cell lines. During cell line establishment there are a lot of things changing inside the cell, particular clones star ...
written 3 months ago by ATpoint30
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Comment: C: Creating contrasts which do not include the reference level in limma, edgeR or D
... I think you need a design formula without intercept `(~0 + ...)` see edgeR manual (https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf) p.69 section 4.4.6 ...
written 3 months ago by ATpoint30
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Comment: C: Anbiguous instruction on how to set the blind value in DESeq2's vst function
... What do you find opposing? As PCA is typically the first step in quality control and detection of potential batch effects, one typically sets it to `T` to get a blinded/unbiased view on the data. ...
written 3 months ago by ATpoint30

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Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.

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