Questions tagged [design]

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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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1answer
61 views

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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1answer
64 views

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 ...
2
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1answer
55 views

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 ...
0
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1answer
175 views

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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1answer
89 views

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 , ...
5
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1answer
85 views

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. ...
1
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1answer
106 views

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 ...
0
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1answer
72 views

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 ...
5
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2answers
106 views

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 ...