Questions tagged [design]
The design tag has no usage guidance.
17 questions
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DGE Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
I am performing differential expression analysis using the limma package on DSP GeoMx data, and I have a question regarding the handling of multiple ROIs per core. ...
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Is this the correct method for determining Power at a given alpha, VAF, and coverage threshold?
I'm trying to calculate power at a given VAF, target coverage, and alpha. For example, what would my power be for a 100x coverage site, detecting VAF of 0.10 with an alpha of 0.05. This is what I came ...
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rna seq matrix design hybrids
I am struggling to get my head around the correct design to use for my experiment.
I have RNAseq of 2 pure species (s1, s2) and of the hybrid (h). I aligned all three genotypes to the s1 genomes. I am ...
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Seeking Guidance on Designing DNA Sequences with Specific Criteria
Dear Bioinformatics Community,
I hope you're all doing well. I am currently working on a project that requires designing some 10 nucleotide single-stranded DNAs, (preferably), with specific criteria.
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LAMP primers design software
What software do you use to design LAMP reaction primers for alignment? So far I have been using Primer Explorer v5 but I am looking for some alternatives.
Alignment includes some species from the ...
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Which components must be included in the HDR plasmid?
I am trying to design a plasmid for our knock in experiment and wanted to clarify some technical issues.
I wanted to know exactly which components must be included in the plasmid.
I know that I have ...
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References request: deciding what duplicate samples to include to avoid batch effects with previous studies
Suppose there is cohort with many samples to assay. In phase I of the project, subjects with a certain disease incidence and healthy controls were assayed. Now, in phase II of the project, we are ...
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the model matrix is not full rank : This is a classic question which a biologist face without clear understanding of the model design
Saw this answer biostar. Tried to make my metadata as such but still the
"Error in checkFullRank(modelMatrix) : "
This is my coldata
...
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Comparing AUCs: Discrimination of same Control from different Test Group - paired or unpaired? miRNA
I want to compare two AUCs using a bootstraping method from pROC package (roc.test).
I have done a classification using Logistic Regression and Serum miRNAs as prediction factors. The Controls are in ...
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Setting Contrast for DESeq2 results
This question was also asked on BioStars
I am trying to recreate this heatmap. How would I compare the four variables: Ly49+/- and MOG/MOGSP to get a single heatmap? Thank you for helping me through ...
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Comparing multiple treatments to multiple other treatments in edgeR for simple effects in a complex experimental design
I am working with a RNA-seq data set in maize that has a relatively complex design. There are two levels of treatment A (nitrogen fertilizer level in the field, high or low), two levels of treatment B ...
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How to incorportate RIN values as covariate in the design matrix?
I have been following the last DESeq2 pipeline to perform an RNAseq analysis with a dataset with low rin samples in the experimental (or treated) and high rin on the control ones.
I read a paper in ...
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How I deal with this kind of gene expression comparision
I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example tumor 1 in batch 1 and tumor 1 in batch 2 , ...
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design formula question
I am not sure I am building the proper design formula for the question I want to answer
I have the following samples with three factors; clone, the structure and the condition.
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How do I select a proper design matrix to use in DRIMSeq?
I am trying to use DRIMseq for DTU with 2 treatments on two different strains of an animal model.
How do I select a proper design matrix to use in DRIMSeq ? How I know that one is the correct one to ...
user4936
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Experimental Design for Differential expreression analysis
I have a Normal esophageal Fibroblasts (NOFs) cultured in DMEM media; The same NOF also have been cultured with a tumor sample from a patient named 005 on DMEM media; I have also Cancer Associated ...
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Deciding which samples go in which batch
I have 370 samples to sequence, we probably will end up using only 96 samples per run (due to the barcode with the primers we'll use). This means running 4 batches. To minimize the batch effect I need ...
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