User: Gordon Smyth

gravatar for Gordon Smyth
Gordon Smyth1.1k
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Australia
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http://www.statsci.org...
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5 days, 8 hours ago
Joined:
5 years, 2 months ago
Email:
s****@wehi.edu.au

Joint Head of the Bioinformatics Division at the Walter and Eliza Hall Institute of Medical Research.

My research group created the limma, edgeR, goseq, Rsubread, csaw and diffHic packages, all part of the Bioconductor project.

Posts by Gordon Smyth

<prev • 71 results • page 1 of 8 • next >
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Answer: A: Trainning on NGS
... https://www.bioconductor.org/packages/release/BiocViews.html#___Workflow ...
written 11 days ago by Gordon Smyth1.1k
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Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
... #Postdoctoral Scientist, Statistical Bioinformatics and Proteomics **Colonial Foundation Healthy Ageing Centre** **The Walter and Eliza Hall Institute of Medical Research** **Parkville, Australia** An excellent opportunity exists for a Statistical Bioinformatician to join the Colonial Foundation H ...
proteomics job written 15 days ago by Gordon Smyth1.1k
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Answer: A: Voom with QuSAGE
... `qusage()` doesn't seem to use precision weights, and that would indeed be a problem if used on the output from `voom()`. You could use `camera()` however, which does use precision weights, and which is much less conservative now than when the QuSAGE paper was published. ...
written 4 weeks ago by Gordon Smyth1.1k
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Answer: A: Analyzing normalized microarray data
... Generally speaking, it is better to get the raw microarray data from your core facility and allow limma to read and normalize the raw files. Then you know what is happening. If you must work with the already processed csv file, then just read it into R using `read.csv`. You will have to wrangle it ...
written 6 weeks ago by Gordon Smyth1.1k
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Answer: A: Remove glmLRT rows under a certain pValue
... We try to document our software in such a way that you don't need to search for explanations, let alone searching for hours. Just type ?glmTreat to bring up the help page. If the short explanation on the help page isn't enough, then read the reference that is cited. Reading the help page would als ...
written 6 weeks ago by Gordon Smyth1.1k
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Answer: A: deseq2 or edgeR
... edgeR and DESeq2 both apply shrinkage to the logFCs, but the default shrinkage applied by edgeR is (deliberately) light touch whereas the DESeq2 shrinkage is heavier. So logFCs from edgeR will often be larger than those from DESeq2 and the result you see is to be expected. This is an example of why ...
written 8 weeks ago by Gordon Smyth1.1k
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Comment: C: Would this laptop be futureproof for bioinformatics work
... Subread can go as low as 8Gb RAM for full genome alignments using a gapped index: https://doi.org/10.1093/nar/gkz114 ...
written 9 weeks ago by Gordon Smyth1.1k
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Comment: C: How to normalized TPM with TMM method?
... I don't know what you are referring to when you say that you "tried it", or what type of data you have applied it to, or what you mean by "some improvement". I am not going to continue this discussion. I have tried to answer OP's question as completely as I can. I have nothing to add to what I have ...
written 3 months ago by Gordon Smyth1.1k
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Answer: A: how to caculate effective length for RNA sequencing?
... If you are doing a gene-level analysis, then I recommend you simply use the gene length values that come from `featureCounts`. The concept of *effective length* is for transcripts rather than genes and is not so clearly relevant for an analysis of gene-level counts from `featureCounts`. However, if ...
written 3 months ago by Gordon Smyth1.1k
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Comment: C: How to normalized TPM with TMM method?
... TMM normalizes library sizes and can only be applied to counts. Any downstream quantity such as CPMs or TPMs that are computed from library sizes will obviously incorporate the TMM normalization, but that is not the same thing as trying to estimate the TMM factors from the CPMs or TPMs. In my opini ...
written 3 months ago by Gordon Smyth1.1k

Latest awards to Gordon Smyth

Teacher 21 days ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Guru 4 weeks ago, received more than 100 upvotes.
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 4 weeks ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Scholar 4 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 8 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Scholar 8 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Scholar 8 months ago, created an answer that has been accepted. For A: Differential expression: replicates in one condition, no replicates in the other
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Differential expression: replicates in one condition, no replicates in the other
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: edgeR - DE with one disease sample vs. multiple control samples?
Scholar 8 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Autobiographer 9 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Scholar 9 months ago, created an answer that has been accepted. For A: DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: published array data not replicable with limma analysis

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