Moderator: Charles Warden

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Charles Warden7.4k
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Duarte, CA
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I am a Bioinformatics Specialist at City of Hope, where I work in the Integrative Genomics Core doing microarray and high-throughput sequencing analysis.

However, the feedback that I provide represent my own personal opinions.

Posts by Charles Warden

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Answer: A: RNA-seq Differential expression analysis show no differentially expressed genes
... I agree with checking overall clustering, as well as increasing the FDR cutoff and/or filtering genes that were not expressed. That said, you are sometimes not going to be able predict which method you need to use ahead of time. So, it sounds like there may be value in testing other methods (like ...
written 14 hours ago by Charles Warden7.4k
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Answer: A: Is there an R package that pulls up gene functional annotations with gene symbol
... Even though I tend to use the [web-interface][1], I believe you can accomplish what you want with the R-package for Enrichr: https://cran.r-project.org/web/packages/enrichR/index.html The only caveat is that you'll need to know which gene sets you want to test ahead of time (instead of browsing th ...
written 14 hours ago by Charles Warden7.4k
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Controlled Access Database for Human Samples Collected after 1/25/2015 (without informed consent for genomic data deposit)?
... My understanding is that there is currently *no situation* where genomic data can be deposited publicly without "*explicit consent*" (regarding the data deposit). I think that is discussed in this [Genomic Data Sharing (GDS) PDF][1], but I am trying to double-check if there is something that specif ...
informed consent data deposit gds ega dbgap written 3 days ago by Charles Warden7.4k
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Answer: A: Machine learning using microarray data
... That is a fairly common microarray platform (for the training set) - I wonder if there might be some formatting issue with the data entry. Yes - if you are getting an essentially random AUC on an independent dataset, then machine learning may not be the best option for your analysis. Likewise, if ...
written 7 days ago by Charles Warden7.4k
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Comment: C: Drug resistant vs. Drug sensitive data retreival from TCGA
... Kevin is right, but I think you need to be able to make sure that you are careful about making sure that you understand the metadata. For example, I think the clinical data is usually after the 1st bio-specimen collection. So, if you were looking for pre-existing changes (before treatment), then t ...
written 10 days ago by Charles Warden7.4k
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Answer: A: Possible Ideas for Citizen Science Project
... I think comparing genomics results for different companies is important, although it may not be exactly "Citizen Science" People can already participate in things like the [FDA MedWatch][1], [PatientsLikeMe][2], and/or the [Personal Genome Project][3] (where I have provided by own page, for an exam ...
written 10 days ago by Charles Warden7.4k
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Comment: C: How to automate bcl2fastq such that it is launched every time the run finishes o
... Thank you for the suggestion - I have accordingly converted the answer to a comment. ...
written 12 days ago by Charles Warden7.4k
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Comment: A: How to automate bcl2fastq such that it is launched every time the run finishes o
... It is good to know how you could automate automatic running of bcl2fastq, but I have encountered a few reasons why you may still need to run some base calling via command line: **1)** If you have multiple library types (such as single-barcode, dual-barcode, 10X samples, custom UMI libraries, etc.). ...
written 12 days ago by Charles Warden7.4k
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Answer: A: Different number of peaks between biological replicates?
... What if you merge the .bed files, and quantify counts within the peaks? Do you get a high correlation in the quantifications? In your case, I think there is some bigger difference (for HTH3), but that is what I would probably check if the peak counts were similar but in different positions (like f ...
written 18 days ago by Charles Warden7.4k
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Comment: C: edgeR gives no DE genes <0.05 FDR
... I think this is very important - you need to critically assess your results. Even if there is a way that essentially forces the data to look like you want, you need some way to show that your result is not horribly over-fit (and not actually reproducible in independent experiments / cohorts). That ...
written 28 days ago by Charles Warden7.4k

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