Moderator: Steve Lianoglou

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Steve Lianoglou4.8k
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I am a computational biologist at Genentech working in Cancer Immunology.

Posts by Steve Lianoglou

<prev • 281 results • page 1 of 29 • next >
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Comment: C: Everything significant in Limma for Differential Expression
... I'm glad that you found your mistake, however I just want to mention that the code you provided in your original post could never have resulted in calling the "coef for the intercept". You said your call to topTable was like so: a <- topTable(fit, n=Inf, adjust="fdr") and if you don't explicit ...
written 22 months ago by Steve Lianoglou4.8k
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Comment: C: Everything significant in Limma for Differential Expression
... Take a look at the help page for ?lmFit, where the documentation for the first parameter (your edata1 object) reads: A matrix-like data object containing log-ratios or log-expression values for a series of arrays, with rows corresponding to genes and columns to samples. Any type of data object that ...
written 22 months ago by Steve Lianoglou4.8k
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Answer: A: Everything significant in Limma for Differential Expression
... This is not easy to diagnose without more information from you, but things that would help include: where did you get your data from? how did you load, process, and, normalize your data? You don't have to provide the data, but you can show us the code you used to do the steps above. The logFC ...
written 22 months ago by Steve Lianoglou4.8k
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Comment: C: Differential gene expession analysis in cell populations of mixed tumor and norm
... I'm curious what you are referring to here. Do you mean the "signal" (counts) you get per gene within sample are not independent in RNA-seq but they are in microarray? Is this "self-evident" because RNA-seq is inherently a competitive assay (since each gene is "competing" for read counts given the ...
written 2.1 years ago by Steve Lianoglou4.8k
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Comment: C: Venn/Euler Diagram Of Four Or More Sets
... I know this is an old post, but for posterity: UpSetR is an R implementation of "UpSet: Visualization of Intersecting Sets". It generates plots like this: ...
written 2.3 years ago by Steve Lianoglou4.8k
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Comment: C: desktop bioinformatics platform specs
... Your specs seem reasonable, and  +1 on Cyril's suggestion for the SSD root/boot drive. ...
written 2.4 years ago by Steve Lianoglou4.8k
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Answer: A: What is the best way to get help on Bioconductor packages?
... As Dan mentioned in his answer on the bioconductor support site, just post the question on the support site and tag it with the name of the package. They have implemented "maintainer integration with the support site" which tries very hard to tickle the listed maintainer of the package via email whe ...
written 2.4 years ago by Steve Lianoglou4.8k
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Answer: A: 3'-Seq // Poly-A seq
... Since you've asked, I would (obviously) choose 3'-seq ;-) But why stop at inquiring about those two? (It would help if you provided references to the protocols you are talking about, as it's not quite clear which protocols you are referring to, by name) There are many more sequencing protocols tha ...
written 2.5 years ago by Steve Lianoglou4.8k
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Answer: A: what was represented by preprocessed RNAseq data provided by ucsc cancer genome
... Select the "About Dataset" options from the "Tools" button to find out more about the dataset. It's not clear what is not convenient (and therefore "not doable") about joining the google group to ask directed questions about the TCGA data in the UCSC browser, but I found this answer myself by just ...
written 2.6 years ago by Steve Lianoglou4.8k
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Answer: A: Match peptides to protein sequences and tell the position in R
... The Biostrings package has many facilities for pattern/string matching. The Multiple Alignments and Pairwise Sequence Alignments vignettes would be useful to read through as a starting point. As for getting sequences straight from UniProt, the answer to that is also yes. The UniProt website has a s ...
written 2.7 years ago by Steve Lianoglou4.8k

Latest awards to Steve Lianoglou

Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: How To Turn A Two Column Data File Containing Pairs Into A Matrix With Counts
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: How To Turn A Two Column Data File Containing Pairs Into A Matrix With Counts
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Publish Our Own Project
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: How To Turn A Two Column Data File Containing Pairs Into A Matrix With Counts
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: How To Turn A Two Column Data File Containing Pairs Into A Matrix With Counts
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: How To Turn A Two Column Data File Containing Pairs Into A Matrix With Counts
Scholar 2.4 years ago, created an answer that has been accepted. For A: R DESeq: What exactly is Variance Stabilizating Transformation?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: How To Turn A Two Column Data File Containing Pairs Into A Matrix With Counts
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: Publish Our Own Project
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: Publish Our Own Project
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How To Turn A Two Column Data File Containing Pairs Into A Matrix With Counts
Scholar 2.8 years ago, created an answer that has been accepted. For A: R DESeq: What exactly is Variance Stabilizating Transformation?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: How To Turn A Two Column Data File Containing Pairs Into A Matrix With Counts
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Reads Per Contig From Sam File?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: How To Turn A Two Column Data File Containing Pairs Into A Matrix With Counts
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Visualizing Chip-Seq And Bis-Seq (Dna Methylation) Data

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