User: mforde84

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Posts by mforde84

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Planned comparison with a ridge regression.
... I have a data set that consists of 1 response variables (e.g., response time) and 20-30 predictors variables with a mixture of categorical and continuous data. I code the categorical data into dummy variables, split the data into training and test sets, then perform a ridge regression on the trainin ...
contrast regression written 8 weeks ago by mforde841.2k
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Comment: C: [IMMEDIATE JOB OPENING] HPC Systems Administrator, Center for Research Informati
... Argonne did a report on this to those interested: https://science.energy.gov/~/media/ascr/pdf/program-documents/docs/Magellan_Final_Report.pdf It's a bit dated admittedly. However, overall operating costs for cloud are still likely 10x+ more expensive then traditional HPC environments. Sure, CRI ha ...
written 11 months ago by mforde841.2k
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Comment: C: [IMMEDIATE JOB OPENING] HPC Systems Administrator, Center for Research Informati
... I mean were talking about tens of millions of proc hours, frequently with large memory requirements, sql services, research grade gpus, petabytes of storage, etc. I doubt AWS would even be competitive, and even if they were close youd end up spending enough renting the infrastructure, that you could ...
written 11 months ago by mforde841.2k
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Comment: C: [IMMEDIATE JOB OPENING] HPC Systems Administrator, Center for Research Informati
... but really, and not drinking the koolaid over here, uchicago is a great place to work. fantastic culture with chill environment and meaningful work. would highly recommend to anyone. i do think that management structure can be a little flat, but that's not always a bad thing. it's just a different t ...
written 11 months ago by mforde841.2k
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Comment: C: [IMMEDIATE JOB OPENING] HPC Systems Administrator, Center for Research Informati
... Sure, people do it. I think you definitely pay for it above and beyond whats really required to provide HPC services to a group of researchers. ...
written 11 months ago by mforde841.2k
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Comment: C: [IMMEDIATE JOB OPENING] HPC Systems Administrator, Center for Research Informati
... No tension really. I believe CRI is headed by Bob as well, if I'm not mistaken. Wasn't always too clear on how upper leadership actually works. Just two different groups, services, and ways to orchestrate them. Would be nice to integrate more with GDC as I think it's a valuable resource, and I know ...
written 11 months ago by mforde841.2k
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Comment: C: How to filter normalized RNA-Seq transcripts for the purpose of predicting a con
... General speaking I'd filter all genes with 0 sum counts, and average CPM/TPM/RPKM/FPKM less than 1. Then normalize filtered counts for library size and between subject variance. Limma voom is very good for this application and can incorporate quality weights for sequencing libraries. Then for regres ...
written 20 months ago by mforde841.2k
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Job: Bioinformatics role becoming available at University of Chicago
... Hi everyone, I'm transitioning to a new role at the University of Chicago, and looking to help find a replacement for my bioinformatics position within the Department of Radiation Oncology. We work primarily with clinical sequencing and microarray of patient samples, immortalized cell lines, and xe ...
genome ngs microarray job written 22 months ago by mforde841.2k • updated 22 months ago by ankur.chaturvedi1719870
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Comment: C: How to select tumor GO terms, if I did not find any in my biological process GO
... There's a lot of biological processes implicated in tumor biology. GO isn't really going to tell you which ones are tumor biology or not (except in a small number of situations). You need to be familiar with the literature and understand which biological processes are implicated in tumor biology, as ...
written 23 months ago by mforde841.2k
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Comment: C: Merge fastq reads for several samples
... maybe im just being too literal here, but he seems to be saying that he's merging reads from two independent runs. and if thats the case, then he probably should be treating each run as a technical replicate, or consider merging after correcting for batch effects. ...
written 23 months ago by mforde841.2k

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Popular Question 10 months ago, created a question with more than 1,000 views. For Hypergeometric GO analysis? and network diagram of generated GO terms
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Popular Question 10 months ago, created a question with more than 1,000 views. For Quantile normalizing prior to or after TPM scaling?
Popular Question 10 months ago, created a question with more than 1,000 views. For Gene level from transcript level expression estimate.
Scholar 10 months ago, created an answer that has been accepted. For A: SNP analysis based on RNAseq data using GATK PIPELINE
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