User: gracechappell

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Posts by gracechappell

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correcting for a batch in DESeq2
... Hello, I have the following experimental design for an experiment in which we conducted RNA sequencing: 2 treatment groups and 2 batches, but one of the batches is exclusively one treatment.  sample    treatment    batch 3    control    A 4    control    A 5    control    B 6    control    B 7    ...
R rna-seq written 4.0 years ago by gracechappell60 • updated 4.0 years ago by Martombo2.5k
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Answer: A: How to add Log2FoldChange as an argument for plotMA in DESeq2
... Thanks for the reply, Vivek.  I'd like to retain the non-significant points in my plot as grey.  By subsetting I only plot those that meet my criteria.    ...
written 4.0 years ago by gracechappell60
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How to add Log2FoldChange as an argument for plotMA in DESeq2
... Hello, I would like to add an argument to the plotMA function in DESeq2.  Specifically, I would like to highlight points on the MA plot that are not only alpha<0.1, but also log2FoldChange <-1 or >1.  Is there a way to achieve this?  I tried the following "ifelse" statement but it did not ...
deseq2 written 4.0 years ago by gracechappell60
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Comment: C: DESeq2 model design: dose and time effect
... Hello, I have a nearly identical experimental design as imsharmanitin; 2 treatment groups and 2 batches, but one of the batches is exclusively one treatment.  sample    treatment    batch 3    control    A 4    control    A 5    control    B 6    control    B 7    control    B 13  control    B 14  ...
written 4.0 years ago by gracechappell60

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Popular Question 4.0 years ago, created a question with more than 1,000 views. For correcting for a batch in DESeq2

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