Moderator: andrew.j.skelton73

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Posts by andrew.j.skelton73

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Comment: C: WGCNA Co-expression network analysis on cuffdiff output
... What have you tried to solve your WGCNA question? ...
written 3 days ago by andrew.j.skelton735.3k
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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 - Also beware that CuffDiff / Tophat2/ Cufflinks have been superseded by HISAT2 / Stringtie / Ballgown.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 4 days ago by andrew.j.skelton735.3k
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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 4 days ago by andrew.j.skelton735.3k
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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 10 days ago by andrew.j.skelton735.3k
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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 10 days ago by andrew.j.skelton735.3k
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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 10 days ago by andrew.j.skelton735.3k
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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 10 days ago by andrew.j.skelton735.3k
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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 10 days ago by andrew.j.skelton735.3k
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Comment: C: Error while doing EdgeR fro miRNA Seq analysis
... This doesn't look like traditional edgeR within the R environment. Can you clarify how you're executing edgeR? ...
written 14 days ago by andrew.j.skelton735.3k
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Comment: C: Lead Bioinformatician at Kew Gardens, Richmond UK
... Is there an email address for informal enquiries? ...
written 5 weeks ago by andrew.j.skelton735.3k

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Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: Find SNPs in the exome from WGS data
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Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Scholar 10 days ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Ensembl biomaRt Down?
Teacher 11 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 11 weeks ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Find SNPs in the exome from WGS data
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Scholar 12 weeks ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
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Commentator 3 months ago, created a comment with at least 3 up-votes. For C: normalization with DEseq2
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Scholar 3 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: normalization with DEseq2
Scholar 3 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
Scholar 3 months ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
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?
Popular Question 4 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?
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

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