User: Kristin Muench

gravatar for Kristin Muench
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kristin_muench
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Posts by Kristin Muench

<prev • 95 results • page 1 of 10 • next >
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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 days ago by Kristin Muench310 • updated 3 days ago by h.mon19k
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Answer: A: Heatmap with normalised count from DESEQ2
... I've used scale() with scale=TRUE, center=TRUE on rlog-normalized, which is a bit like z-score. I've seen people also plot log-scaled expression values too. One tip - if you use asinh() instead of log2(), you can create the same kind of scaling, but you don't have to add 1 in order to account for p ...
written 4 days ago by Kristin Muench310
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[DESeq] Collapsing replicate across sequencing batches?
... Hello, My colleague performed a 3' RNA-Seq experiment twice. She ran a subset of these samples twice. Can I collapse these like technical replicates using the DESeq collapseReplicates()? If not, should I remove them from my study because 'doubling up' on samples will bias the results? When I say s ...
deseq rna-seq written 4 days ago by Kristin Muench310
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Comment: C: Normal to have high variability in Broad Institute's GSEA Output?
... I did! The data is puzzling because the effect seems to be of a different magnitude on FDR q-values vs. other types of metrics generated by GSEA. Code: # Set up dataset varsToSave <- c('NAME', 'NOM p-val', 'FWER p-value', 'RANK AT MAX', 'FDR q-val') plotData <- merge(round1[ ...
written 10 days ago by Kristin Muench310
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Comment: C: Normal to have high variability in Broad Institute's GSEA Output?
... The way the GUI is set up you do not have the option to set a FDR pre-run - rather, it generates a new leading edge analysis each time, and then you set the FDA when interpreting the list/deciding what to visualize (although, in my case, the list would still be different each time, even if you do ch ...
written 10 days ago by Kristin Muench310
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Comment: C: Normal to have high variability in Broad Institute's GSEA Output?
... That is correct - I am running MIT/Broad's Java Application (64 bit 8 GB version for Mac). I imported the necessary files in once, clicked the "GSEAPreranked" tab, set up the appropriate files in the drop-down boxes, then pressed "Run" - then waited for that to run - then when it finished, pressed " ...
written 10 days ago by Kristin Muench310
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Normal to have high variability in Broad Institute's GSEA Output?
... I am doing a Preranked GSEA Analysis on the output of a differential expression analysis (genes ranked by sign(shrunken lfc) * -log10(pvalue) ). I notice that when I feed the exact same files into GSEA, it can give me fairly different FDRs. For example, when I ran the analysis the first time, it s ...
gsea go written 11 days ago by Kristin Muench310
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Comment: C: Visualizing alignment of kallisto .bam files to hg19 (and custom plasmids)
... Thank you again for your suggested tips. I tried editing my gtf, removing the samview portion of my kallisto quant line, and re-running the pipeline. This time, I did it both the original way (trying to build index from plasmid+ transcriptome) as well as a simplified vdrsion (trying to build index f ...
written 12 days ago by Kristin Muench310
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Comment: C: Visualizing alignment of kallisto .bam files to hg19 (and custom plasmids)
... Thank you for this extremely helpful answer! I'll give it a try! ...
written 15 days ago by Kristin Muench310
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Comment: C: Visualizing alignment of kallisto .bam files to hg19 (and custom plasmids)
... Thanks for pointing out where it's falling down. You actually can use IGV with kallisto now: https://pachterlab.github.io/kallisto/pseudobam.html https://twitter.com/lpachter/status/958130098430857216?lang=en ...
written 15 days ago by Kristin Muench310

Latest awards to Kristin Muench

Popular Question 13 days ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 3 months ago, created a question with more than 1,000 views. For Is it problematic to use ANOVA in microarray meta-analysis?
Popular Question 3 months ago, created a question with more than 1,000 views. For Why can't I replicate DESeq's Log2FC calculation?
Popular Question 5 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 7 months ago, created a question with more than 5,000 views. For Bowtie2: Why won't it recognize my index files?
Supporter 7 months ago, voted at least 25 times.
Popular Question 14 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 14 months ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Popular Question 14 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 14 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 14 months ago, created a question with more than 1,000 views. For Is it possible to compare 3SEQ and RNA-Seq data?
Great Question 21 months ago, created a question with more than 5,000 views. For Bowtie2: Why won't it recognize my index files?
Popular Question 21 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 2.3 years ago, created a question with more than 1,000 views. For Determining gene expression with 2 biological replicates and RPKM data only

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