Questions tagged [design]

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6 votes
2 answers
146 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 ...
llrs's user avatar
  • 4,703
5 votes
1 answer
102 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. ...
mario rossi's user avatar
3 votes
1 answer
189 views

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 ...
kcm's user avatar
  • 1,804
2 votes
1 answer
401 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 ...
Eddie's user avatar
  • 21
1 vote
1 answer
185 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 ...
user avatar
1 vote
1 answer
31 views

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 ...
RomainL.'s user avatar
  • 145
1 vote
1 answer
34 views

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. ...
Hashem's user avatar
  • 11
1 vote
0 answers
19 views

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 ...
Research HMBR's user avatar
0 votes
1 answer
615 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 ...
FrAoJm's user avatar
  • 37
0 votes
1 answer
224 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 ...
Mahejabeen Nidhi's user avatar
0 votes
1 answer
93 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 , ...
Zizogolu's user avatar
  • 2,148
0 votes
1 answer
77 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 ...
Zizogolu's user avatar
  • 2,148
0 votes
0 answers
37 views

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 ...
pourpre's user avatar
0 votes
1 answer
41 views

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 ...
wdg's user avatar
  • 101
0 votes
1 answer
70 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 ...
Mischa's user avatar
  • 13