Understanding DESeq2 design, contrast and results
dds = DESeq(dds, test="LRT" reduced=~geno+geno:Treatment) The above would give you results for Treatment regardless of level while still accounting for a possible interaction (i.e., a "main effect of treatment, regardless of the type of treatment").
How can I extract normalized read count values from DESeq2 …
DESeq for instance does not use either rlog or vst for its test of differential expression, as these would be inappropriate. $\endgroup$ – Konrad Rudolph Commented Jan 29, 2019 at 12:13
Adjusted P-value from DESeq2 - Bioinformatics Stack Exchange
2021年8月11日 · Stack Exchange Network. Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.
nested samples in design DEseq2 - Bioinformatics Stack Exchange
2022年7月25日 · then everything goes well and I'm able to create a DESeq object with the following design: ddsMat <- DESeqDataSetFromMatrix( countData = as.matrix(matrix[,1:6]), colData = coldata2, design = ~ class+Pts ) Please can you provide to me some suggestion on how to solve the problem? Thank you
deseq2 full and reduced model interpretation
2022年5月30日 · test.Age <- as_tibble(results(DESeq(dds, test="LRT", reduced= ~Sex + Age ))) Now my question is since I'm using the same dds object here where the FAB is the variable i fixed and with new formula which is. reduced= ~Sex + Age this so how would i interpret this model? Any suggestion or help would be really appreciated
DEseq2 contrast in two time points - Bioinformatics Stack Exchange
2021年10月8日 · I need help with some clarifications please I have control versus treatment in two time points like > y X condition time 1 CTRL_24_hrs_replicate1 control 2...
DESeq2 for large number of samples takes too much RAM
2022年12月20日 · The above steps should take less than 30 seconds for most analyses. For experiments with complex designs and many samples (e.g. dozens of coefficients, ~100s of samples), one may want to have faster computation than provided by the default run of DESeq. We have two recommendations:
Is it possible to do DEG analysis without replicates?
2021年9月17日 · I have three bulk RNA-seq samples (test1, test2, test3) without replicates. And I noticed that DEG analysis tools such as DESeq2/edgeR/etc cannot be applied for data with no replicates.
Install DESeq2 through anaconda - Bioinformatics Stack Exchange
Stack Exchange Network. Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.
Use of "baseMean" in DeSEQ2 - Bioinformatics Stack Exchange
2021年12月30日 · Stack Exchange Network. Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.