Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
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Genentech
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Joined:
7 years, 9 months ago
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I am a Computational Biologist at Genentech working in Cancer Immunology.

In a previous life, I was studying alternative cleavage and polyadenylation in humans.

Posts by Steve Lianoglou

<prev • 1,329 results • page 1 of 133 • next >
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Answer: A: Dr. Armin Ahmadvand
... I would guess your Negin_AD_BD objet isn't what you think it is. It needs to be a numeric matrix, with no missing values. Check the output of the following: class(Negin_AD_BD) (is it matrix?) class(Negin_AD_BD[1]) (is it numeric?) any(is.na(Negin_AD_BD)) (is it FALSE?) Also, you'll probably ...
written 2 days ago by Steve Lianoglou12k
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Answer: A: Limma filtering based on treatment group
... No. Don't do that. Your filtering criterion needs to be independent of the test statistic:  http://m.pnas.org/content/107/21/9546.long     ...
written 6 days ago by Steve Lianoglou12k
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Comment: C: Is mapId supposed to concatenate multiVals?
... Thanks for the quick feedback, James and Johannes. FWIW, in the meantime I'm going with using biomaRt to map these ... turns out Tceb1 is actually called Eloc now anyways ;-)   ...
written 9 days ago by Steve Lianoglou12k
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Is mapId supposed to concatenate multiVals?
... I used the AnnotationDbi::mapIds function over the EnsDb.Mmusculus.v79 package to map Ensembl Gene IDs back to entrez id over a a long vector of ENSG Ids. I expected this to return a 1:1 mapping when mapIds(..., multiVals='first'), but was surprised that this returned several entrez ids concatenate ...
annotationdbi ensembldb written 9 days ago by Steve Lianoglou12k • updated 9 days ago by James W. MacDonald43k
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Comment: C: unable to get tximport to work on data from kallisto
... What do you mean "run multiple files at a time?" Sorry if I'm being obtuse but I have no idea what you might be referring to. Can you provide more context to the question? ...
written 12 days ago by Steve Lianoglou12k
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Answer: A: unable to get tximport to work on data from kallisto
... Look at the sequence file you used to generate your kallisto index. Are the IDs (names) of the transcript sequences in there the same as the names you extracted from the EnsDB? A common mistake is the use of "versioned" ensmble transcript identifiers in one source or the other, ie. one has ENST0000 ...
written 12 days ago by Steve Lianoglou12k
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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... The suspicious thing for me is that you needed to do some manual munging/merging of the two datasets and account for NAs after that, which tells me that there were some genes that were quantitated on one side that weren't in the other (or vice versa). All things being equal, if you're working with ...
written 20 days ago by Steve Lianoglou12k
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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... Were your two batches of data quantitated using the same pipeline? ...
written 20 days ago by Steve Lianoglou12k
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Comment: C: Using voomWithQualityWeights for differential expression analysis.
... As a side note: you mention that you removed genes with zero counts (although you didn't show in your core). You will probably have to filter out a bit more than that. Make sure that you inspect the voom variance:mean plot that is produced when you call voomWithQualityWeights(...., plot=TRUE). ...
written 5 weeks ago by Steve Lianoglou12k
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Comment: C: Calculate correlation matrix for gene expression data
... install.packages won't work. You can only install bioconductor packages using the biocLite function from the BiocInstaller package. These instructions can be found on the Install page on the Bioconductor website, as well as the "Installation" section of each of the packages you are trying to insta ...
written 6 weeks ago by Steve Lianoglou12k

Latest awards to Steve Lianoglou

Scholar 6 days ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 13 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 13 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 13 months ago, created an answer that has been accepted. For A: Filtering after a contrast
Teacher 13 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 13 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 15 months ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Guru 15 months ago, received more than 100 upvotes.
Scholar 15 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 19 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Scholar 22 months ago, created an answer that has been accepted. For A: "Wobble" patterns for genome searching using Biostrings
Scholar 2.0 years ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Scholar 2.2 years ago, created an answer that has been accepted. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Oracle 2.3 years ago, created more than 1,000 posts (questions + answers + comments).
Voter 2.3 years ago, voted more than 100 times.
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis

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