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Moderator: andrew.j.skelton73

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Posts by andrew.j.skelton73

<prev • 681 results • page 1 of 69 • next >
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Comment: C: ATYPICAL VOLCANO PLOT RNA SEQ
... It would be helpful if you included code for your analysis, did you use `lfcShrink`? Are your samples all from the same experiment? What did you PCA show? ...
written 8 days ago by andrew.j.skelton73 ♦ 5.4k
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Answer: A: eQTL analysis considering P-values
... For generic QTL analyses, I'd recommend the MatrixEQTL package and associated methodology. It's blazing fast providing you have the right LINPACK libraries. [Website][1] / [Paper][2] / [Package (CRAN)][3] Check out the website for some useful examples and configurations [1]: http://www.bios. ...
written 10 days ago by andrew.j.skelton73 ♦ 5.4k
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Comment: C: WGCNA Co-expression network analysis on cuffdiff output
... What have you tried to solve your WGCNA question? ...
written 8 weeks ago by andrew.j.skelton73 ♦ 5.4k
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Comment: C: WGCNA Co-expression network analysis on cuffdiff output
... What have you tried? - Also beware that CuffDiff / Tophat2/ Cufflinks have been superseded by HISAT2 / Stringtie / Ballgown. ...
written 8 weeks ago by andrew.j.skelton73 ♦ 5.4k
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Comment: C: transcription expression matrix for DESEQ2
... In this case, it's probably worth contacting the author, or looking at potentially more detailed methods in the supplementary. Keep in mind, "*just because you can, doesn't mean you should*" - It's worth critically assessing what DESeq2 requires as inputs, against what they've provided from bitSeq. ...
written 8 weeks ago by andrew.j.skelton73 ♦ 5.4k
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Answer: A: transcription expression matrix for DESEQ2
... bitSeq is more an all in one for differential transcript expression. You wouldn't be able to input those estimates into DESeq2, I'd recommend following one of these methodologies if you want to do differential gene expression or differential transcript expression from the same quantifications: **S ...
written 9 weeks ago by andrew.j.skelton73 ♦ 5.4k
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Comment: C: transcription expression matrix for DESEQ2
... Where did this expression matrix come from? - You can provide matrix input for DESeq2, but this must be integer counts of genes. For transcript level count estimates, you need to follow the [tximport][1] protocol, from either Salmon or Kallisto. [1]: https://bioconductor.org/packages/release/bio ...
written 9 weeks ago by andrew.j.skelton73 ♦ 5.4k
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Comment: C: WGCNA-consensus network analysis using RNA-seq data
... If these are from different experiments, then that's a whole different box of questions. Normalising cross experiment is far from trivial, and can only be done in some cases. The big caveat for WGCNA is that you need a decent number (>20) of samples to get interpretable output. If these are cro ...
written 9 weeks ago by andrew.j.skelton73 ♦ 5.4k
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Answer: A: Is it possible to make a PCA plot for samples using TPM exprssion values in R?
... You should transform your data to a log-like scale. If you're analysing in DESeq2, look at `vst` or `rlog` methods, alternatively if you're using `Limma Voom`, then your data should be good to go. Have a look at the [tximport][1] package if you're confused about these different input metrics. When ...
written 9 weeks ago by andrew.j.skelton73 ♦ 5.4k
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Answer: A: WGCNA-consensus network analysis using RNA-seq data
... For use in WGCNA, your data should be log2-like, so [vst][1] or [rlog][2] transformations are appropriate. Alternatively, you could use [Limma Voom][3] too for RNAseq data. [1]: https://rdrr.io/bioc/DESeq2/man/varianceStabilizingTransformation.html [2]: https://rdrr.io/bioc/DESeq2/man/rlog.ht ...
written 9 weeks ago by andrew.j.skelton73 ♦ 5.4k

Latest awards to andrew.j.skelton73

Scholar 12 days ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Scholar 20 days ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Great Question 26 days ago, created a question with more than 5,000 views. For Illumina Instrument Type from fastq?
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Find SNPs in the exome from WGS data
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Find SNPs in the exome from WGS data
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Popular Question 3 months ago, created a question with more than 1,000 views. For Ensembl biomaRt Down?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Scholar 4 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Find SNPs in the exome from WGS data
Appreciated 4 months ago, created a post with more than 5 votes. For A: Find SNPs in the exome from WGS data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Scholar 4 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Appreciated 4 months ago, created a post with more than 5 votes. For A: Find SNPs in the exome from WGS data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: normalization with DEseq2
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Scholar 5 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: normalization with DEseq2
Scholar 5 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Scholar 5 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Popular Question 6 months ago, created a question with more than 1,000 views. For Ensembl biomaRt Down?
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