User: kmuench

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kmuench30
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Posts by kmuench

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Comment: C: Handling biological replicates across batches in DESeq2
... Ah, thank you very much for your reply! I'll propagate this back to Biostars and take a look at limma-voom. I appreciate the insight. ...
written 6 weeks ago by kmuench30
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Comment: C: Handling biological replicates across batches in DESeq2
... That said: I would be so happy if collapseReplicates() were appropriate in this situation, because the only other alternative I've found is to try to create a custom design matrix with a separate factor for every set of duplicated samples and feed that into the full= flag of DESeq(), which is very l ...
written 6 weeks ago by kmuench30
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Comment: C: Handling biological replicates across batches in DESeq2
... Sure. My understanding is that technical replicates had to be drawn from the same library preparation/cDNA, not just the same RNA. In my case, a whole new library preparation was prepared in the second batch on the same RNA from the first batch (plus a few extra/new samples thrown in). I imagine tha ...
written 6 weeks ago by kmuench30
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Comment: C: Handling biological replicates across batches in DESeq2
... Ah thank you for the reminder - cross-link complete. ...
written 6 weeks ago by kmuench30
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Handling biological replicates across batches in DESeq2
... Cross-post w/ Biostars based on commenter suggestion: https://www.biostars.org/p/345751/#345776 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 ...
deseq2 written 6 weeks ago by kmuench30 • updated 6 weeks ago by Michael Love20k
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What does this error mean? - issue implementing SVA
... Hello, I'm attempting to implement sva on my RNA-Seq count data matrix. I have a table, myFactors, which describes various potential sources of known (e.g., myFactors$Condition - control, condition1, condition2) and suspected (e.g., myFactors$Date - date of sample preparation) variation. I've foll ...
sva rna-seq written 2.8 years ago by kmuench30 • updated 8 months ago by Sandip Darji0
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Comment: C: Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
... Haha! Thank you for pointing that out! ...
written 3.1 years ago by kmuench30
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Comment: C: Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
... For posterity: my issue is specifically that the library doesn't seem to be available yet for my version of R (error: "package ‘ensembldb’ is not available (for R version 3.1.2)"). Currently working through these possibilities: http://stackoverflow.com/questions/25721884/how-should-i-deal-with-packa ...
written 3.1 years ago by kmuench30
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Comment: C: Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
... Thank you for the suggestion! I'm having trouble with the install (getting a "there is no package called ‘EnsDb.Hsapiens.v75’" message) but this looks like what I want - I'll keep trying. ...
written 3.1 years ago by kmuench30
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Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
... Hello, In R, I previously used this piece of code to look up Ensembl IDs for lists of genes beginning with ENSG000... .  In this example, my_df is a dataframe where the rownames are the gene IDs 9e.g. ENSG...):   my_df$ensembl <- sapply( strsplit( rownames(my_df), split="\\+" ), "[", 1 ) ...
rnaseq biomart R written 3.1 years ago by kmuench30 • updated 3.1 years ago by Johannes Rainer1.3k

Latest awards to kmuench

Popular Question 2.6 years ago, created a question with more than 1,000 views. For What does this error mean? - issue implementing SVA
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
Student 2.6 years ago, asked a question with at least 3 up-votes. For What does this error mean? - issue implementing SVA

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