Bioconductor Liimma

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genefilter liimma microarray

updated 7.9 years ago by Wolfgang Huber 13k • written 7.9 years ago by Shamim Sarhadi ▴ 20

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Answer: Differential gene expression analysis by ATpoint ★ 3.6k

You cannot use genotype and condition in the same model as they're nested, meaning that some genotypes are only on Fast and others are only…

Comment: Deleted:No significant MVPs with a BH adjusted P-value below 0.05 by Basti ▴ 740

There is no problem, there is not any significant DMP between the groups compared.

Comment: Deleted:No significant MVPs with a BH adjusted P-value below 0.05 by 486342583 • 0

I realized that someone had asked the same question, but he seemed to have closed the issue and I didn't see a solution. I hope to receive …

Comment: Help with model.matrix and creating the right contrast matrix for limma by Gordon Smyth 48k

> Does this mean there is an anova test comparing the mean expression of each gene for each contrast specified (LvsC_m5 and HvsC_m5)? So wh…

Comment: TPM to raw counts by bella.johnson.2022 • 0

I know this is a bit of an old thread, but I used `'tximport'` to take my TPM output from Salmon and get the raw counts to then run DESeq2 …

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Comment: Ensembl down???

Comment: Problem loading HDF5Array in R 4.3.2

Answer: gseGO input list

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