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User: Kristin Muench

gravatar for Kristin Muench
Reputation:
350
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Twitter:
kristin_muench
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Joined:
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Posts by Kristin Muench

<prev • 104 results • page 1 of 11 • next >
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Comment: C: Handling biological replicates across batches in DESeq2
... Hello - I posted his reply below, hope it helps ...
written 11 weeks ago by Kristin Muench • 350
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Comment: C: Handling biological replicates across batches in DESeq2
... Thank you for clarifying. I wonder if there might still be an issue that individual samples are correlated to each other that might not be accounted for in the design/might still influence results? Mike Love suggested one strategy (post below) but I think I'll try this to see how much of a differenc ...
written 11 weeks ago by Kristin Muench • 350
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Answer: A: Handling biological replicates across batches in DESeq2
... Hello, Back-propagating the answer that Mike Love suggested on Bioconductor forums: If there is not a lot of technical variation across replicates > consider treating the samples like technical replicates, and collapse them in DESeq using the collapseReplicates() function. If there is a lot of ...
written 11 weeks ago by Kristin Muench • 350
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Comment: C: Handling biological replicates across batches in DESeq2
... Ah thank you! I haven't interacted with Bioconductor forum much, I'll give it a try. ...
written 11 weeks ago by Kristin Muench • 350
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Comment: C: Handling biological replicates across batches in DESeq2
... Ah thank you! This may be the way to go. My concern with combining these factors is that it will make downstream analyses difficult because we are interested in the main effect of each (e.g. overall effect of Genotype, overall effect of Sex) as well as interaction effect (e.g. overall effect of Geno ...
written 11 weeks ago by Kristin Muench • 350
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Comment: C: Handling biological replicates across batches in DESeq2
... Thanks for the suggestion! Unfortunately, it does seem like all of the aforementioned factors do separate within the first two PCs - except for Sex, which we know should absolutely have a large expression difference in all conditions at all timepoints. Replicate samples in non-batch-corrected data u ...
written 11 weeks ago by Kristin Muench • 350
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Handling biological replicates across batches in DESeq2
... EDIT: Cross-posted on Bioconductor: https://support.bioconductor.org/p/114506/ --------- Hello, I am trying to figure out how to handle biological replicates across batches in DESeq2's design matrix. They're not quite technical replicates, but trying to include the sample ID as a factor in the d ...
R deseq2 deseq rna-seq written 11 weeks ago by Kristin Muench • 350
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Comment: C: "Duplicate rownames not allowed" when the rownames are not duplicated
... Thank you for taking a look at this! ...
written 3 months ago by Kristin Muench • 350
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"Duplicate rownames not allowed" when the rownames are not duplicated
... Hello, I'm getting an error from DESeq2 that insists I have duplicates somewhere in my data, but I don't think I do. I loaded transcript data from kallisto using tximport(). I wanted HUGO gene-wise counts, not transcript counts, so I aggregated these and fed the result into a DESeq object using DE ...
deseq2 written 3 months ago by Kristin Muench • 350 • updated 3 months ago by Michael Love • 1.7k
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Comment: C: [DESeq] Collapsing replicate across sequencing batches?
... They do cover all treatments, but not all samples. Would the batch variable look something like: SAMPLE | EXPERIMENT DAY | BATCH ------------ | --------------------------- | ----------- A | Day 1 | Original A ...
written 3 months ago by Kristin Muench • 350 • updated 3 months ago by h.mon ♦ 22k

Latest awards to Kristin Muench

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Handling biological replicates across batches in DESeq2
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Centurion 11 weeks ago, created 100 posts.
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 4 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 7 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 7 months ago, created a question with more than 1,000 views. For Why can't I replicate DESeq's Log2FC calculation?
Popular Question 9 months ago, created a question with more than 1,000 views. For How many reads should I expect for paired end reads when coverage = 30 million?
Great Question 11 months ago, created a question with more than 5,000 views. For Bowtie2: Why won't it recognize my index files?
Supporter 11 months ago, voted at least 25 times.
Popular Question 17 months ago, created a question with more than 1,000 views. For How many reads should I expect for paired end reads when coverage = 30 million?
Popular Question 17 months ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Popular Question 17 months ago, created a question with more than 1,000 views. For Could a "complete" RNA-Seq database feasibly exclude some protein-coding transcripts?
Popular Question 17 months ago, created a question with more than 1,000 views. For Determining gene expression with 2 biological replicates and RPKM data only
Popular Question 17 months ago, created a question with more than 1,000 views. For Is it possible to compare 3SEQ and RNA-Seq data?
Great Question 2.1 years ago, created a question with more than 5,000 views. For Bowtie2: Why won't it recognize my index files?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Determining gene expression with 2 biological replicates and RPKM data only
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Determining gene expression with 2 biological replicates and RPKM data only
Popular Question 2.7 years ago, created a question with more than 1,000 views. For I have demultiplexed files for a single biological replicate. When to combine them in pipeline?
Appreciated 3.0 years ago, created a post with more than 5 votes. For How do I explain to my non-bioinformatician labmates how to interpret principal components?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For I have demultiplexed files for a single biological replicate. When to combine them in pipeline?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For I have demultiplexed files for a single biological replicate. When to combine them in pipeline?
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