Tag: MLE

Condition shown as ‘Untreated vs. Treated’ in output of results() in DESeq2

Condition shown as ‘Untreated vs. Treated’ in output of results() in DESeq2 1 @bffcbc5f Last seen 16 hours ago United States of America I am trying to find differentially expressed genes using DESeq2 on some RNA-seq data. In the pheno data, there is a column named ‘condition’ with factored values…

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Knockdown of circRNA Paralemmin 2 Ameliorates Lipopolysaccharide-induced Murine Lung Epithelial Cell Injury by Sponging miR-330-5p to Reduce ROCK2 Expression: Immunological Investigations: Vol 0, No 0

ABSTRACT Previous data have reported the high expression of circRNA paralemmin 2 (circPALM2) in mice with acute lung injury (ALI). However, the role of circPALM2 in ALI pathogenesis remains unclear. The study aims to reveal the function of circPALM2 in ALI and the underlying mechanism. C57BL/6 J mice and murine lung…

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Large DE LogFC range

Large DE LogFC range 1 @3d20f23f Last seen 1 hour ago Italy I’m working with DESeq2 to make a DE analysis between samples in two different conditions. During the analysis, I identified a batch effect due to the sequencing time modelled as a covariate in the design formula. From the…

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Mle Application With Gekko In Python

The true power of the state space model is to allow the creation and estimation of custom models.This notebook shows various statespace models that subclass sm. That means your MAGeCK python module is installed in /home/john/.pyenv/versions/2.7.13/lib/python2.7/sitepackages.I use conda to install the latest version of. This twovolume set Diseases and Pathology…

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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter

Enter the body of text here Hi, I am analysing a RNA Seq dataset coming from 3 independent cell isolates (isolate1, isolate2, isolate3), each given 3 different treatments (control, drug1, drug2). We are testing drug 1 against control in the first instance: We also observed that there is some variation…

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[Bug 1951032] Autopkgtest regression report (glibc/2.31-0ubuntu9.4)

All autopkgtests for the newly accepted glibc (2.31-0ubuntu9.4) for focal have finished running. The following regressions have been reported in tests triggered by the package: snapd-glib/1.58-0ubuntu0.20.04.0 (armhf) apt/2.0.6 (armhf) libmath-mpfr-perl/4.13-1 (armhf) art-nextgen-simulation-tools/20160605+dfsg-4 (armhf) ruby-nokogiri/1.10.7+dfsg1-2build1 (armhf) r-cran-rgdal/1.4-8-1build2 (armhf) arrayfire/3.3.2+dfsg1-4ubuntu4 (armhf) libpango-perl/1.227-3build1 (armhf) libimage-sane-perl/5-1 (s390x) ruby-bootsnap/1.4.6-1 (arm64) mle/1.4.3-1 (ppc64el, arm64) libsyntax-keyword-try-perl/0.11-1build1 (armhf)…

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Sp.stats and PyMC3 logps different – Questions

Hi everyone, I am fitting a geometric distribution to the following data: [40000, 600, 1500, 30000, 12000, 25000, 65000, 1500, 40000, 10000000, 25000, 2000, 2000, 500, 800, 1500, 30000, 850, 25000, 1000, 15000, 40000, 9000, 3000, 12000, 1000, 1000, 1500, 10000, 25000, 7000, 35000, 30000, 25000, 750, 20000, 7000, 1500,…

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Outliers on DESEq2 Results

I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from 10 to 12, with a few counts > 9000. I process this data in Deseq2 and get that the gene is differentially expressed across several samples of interest. What can…

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Analysis of shRNA/CRISPR screens in 2021

I’ve used Mageck for CRISPR screens and it works great. A few things: It, by default, doesn’t allow mismatches between read and library but still I’ve always had good (>= ~80%) mapping rates; I’ve had better mapping results with paired-end reads (because if one read fails to align because of…

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Handle inflated log2FC while using interaction term in DESeq2

Hi guys, I’m working with a 8 samples experiment (lower than 3x replicates, I know..) with a design like > colData(dds) DataFrame with 8 rows and 2 columns condition traitment <factor> <factor> 4200-JS-1 norm ctrl 4200-JS-2 norm ctrl 4200-JS-3 norm trt 4200-JS-4 norm trt 4200-JS-5 hyper ctrl 4200-JS-6 hyper ctrl…

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Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

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