Moderator: Kevin Blighe

gravatar for Kevin Blighe
Kevin Blighe59k
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59,430
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Website:
https://github.com/kev...
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KevinBlighe
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Last seen:
29 minutes ago
Joined:
2 years, 9 months ago
Email:
k****@clinicalbioinformatics.co.uk

I am from the Republic of Ireland and have worked with dozens of universities, private companies, healthcare providers, and research institutes across the World, effectively functioning as a self-funded, independent research lab.

I contribute to the European Commission as an Expert Monitor, and also Moderate on the Biostars and Bioconductor support communities.
 

Developer / Maintainer of Bioconductor packages:

Other packages:

LinkedIn: https://www.linkedin.com/in/clinicalbioinformatics/

 

Posts by Kevin Blighe

<prev • 8,157 results • page 1 of 816 • next >
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Comment: C: How to simultaneously convert gene IDs to Kegg IDs for E. coli
... For clusterProfiler, you just need Entrez IDs, and you have those via the code that I shared in the previous answer. ...
written 2 hours ago by Kevin Blighe59k
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Comment: C: How to simultaneously convert gene IDs to Kegg IDs for E. coli
... Are you implying that you do not see this output when you run this command [?]: keytypes(org.EcK12.eg.db) [1] "ACCNUM" "ALIAS" "ENTREZID" "ENZYME" "EVIDENCE" [6] "EVIDENCEALL" "GENENAME" "GO" "GOALL" "ONTOLOGY" [11] "ONTOLOGYALL" "PATH" ...
written 3 hours ago by Kevin Blighe59k
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Comment: C: How to perform PCA on gene expression?
... I would not use raw read counts for PCA ...
written 3 hours ago by Kevin Blighe59k
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Answer: A: DeSeq2 error: Every gene contains at least one zero, cannot compute log geometri
... I encountered this error only once in the past. It is as stated: every gene in your data has at least one zero value, and this creates an issue for the size-factor calculation. Solutions: 1. add a pseudo-count value of '1' to your data 2. use: `estimateSizeFactors(dds_PvsN, type = 'iterate')` K ...
written 12 hours ago by Kevin Blighe59k
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Answer: A: retrieve TPM matrix from raw counts matrix or DESeq2 object dds
... I and colleague Asaf gave an answer here: https://www.biostars.org/p/440175/#440368 > I see - thanks. You can calculate TPM from the BRCA_mat object; > however, you will still require the gene lengths. The TPM calculation > is elaborated ere: > https://www.rna-seqblog.com/rpkm-fpkm-and ...
written 14 hours ago by Kevin Blighe59k
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Comment: C: DEXSeq aggregates two different genes together
... Hey Rohit, thanks for coming back to explain - means a lot. Unfortunately, I don't have much to add due to the fact that the last time that I used DEXSeq was in 2016. I imagine that it is very difficult (for any program) to account for every possible splice-configuration, though. For what it's worth ...
written 14 hours ago by Kevin Blighe59k
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Comment: C: error in TXIMPORT command for RSEM
... I see - thanks. You can calculate TPM from the *BRCA_mat* object; however, you will still require the gene lengths. The TPM calculation is elaborated ere: https://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained. DESeq2 does not produce TPM data. However, you could easily use DESeq2 to produ ...
written 14 hours ago by Kevin Blighe59k
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Answer: A: How to simultaneously convert gene IDs to Kegg IDs for E. coli
... Hey again, you have KEGG IDs from my previous answer (see 'PATH' column): https://www.biostars.org/p/439972/#439994 Kevin ...
written 15 hours ago by Kevin Blighe59k
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Comment: C: Design in DESeq: Can you combine explicit and implicit batch effect correction i
... Use `blind=TRUE` for QC (box-and-whiskers, PCA, unsupervised clustering, etc), but `blind=FALSE` for producing data for anything else downstream ...
written 16 hours ago by Kevin Blighe59k
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Comment: C: error in TXIMPORT command for RSEM
... Before we become completely confused here, which data have you downloaded? It has been implied that you have both HT-seq and RSEM data, but these are produced from different methods. Only the HT-seq files will contain a raw count, whereas RSEM files will contain an estimated count. If you literally ...
written 18 hours ago by Kevin Blighe59k

Latest awards to Kevin Blighe

Teacher 18 hours ago, created an answer with at least 3 up-votes. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Scholar 18 hours ago, created an answer that has been accepted. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Scholar 2 days ago, created an answer that has been accepted. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Scholar 2 days ago, created an answer that has been accepted. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Appreciated 3 days ago, created a post with more than 5 votes. For A: Z score in RNAseq
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Scholar 5 days ago, created an answer that has been accepted. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Appreciated 6 days ago, created a post with more than 5 votes. For A: Z score in RNAseq
Scholar 7 days ago, created an answer that has been accepted. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Appreciated 7 days ago, created a post with more than 5 votes. For A: Z score in RNAseq
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Good Answer 8 days ago, created an answer that was upvoted at least 5 times. For A: Alternate nucleotide is more frequent than reference nucleotide. OMG I'm dizzy.
Appreciated 8 days ago, created a post with more than 5 votes. For PCAtools: everything Principal Components Analysis
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Scholar 11 days ago, created an answer that has been accepted. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Scholar 11 days ago, created an answer that has been accepted. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Good Answer 13 days ago, created an answer that was upvoted at least 5 times. For A: Alternate nucleotide is more frequent than reference nucleotide. OMG I'm dizzy.
Appreciated 13 days ago, created a post with more than 5 votes. For Determine % of reference genome covered by aligned SAM/BAM
Scholar 13 days ago, created an answer that has been accepted. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
Popular Question 15 days ago, created a question with more than 1,000 views. For Clustering of DAVID gene enrichment results from gene expression studies
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R

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