User: shawn.w.foley

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Posts by shawn.w.foley

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How to find the gene structure of a gene?
... Can you give more detail about what you're looking for? Are you annotating genes de novo and trying to predict structure? Does structure mean where is the CDS? Are you interested in each exon, and each UTR? Is this a novel organism or are you looking for annotation files? ...
written 5 days ago by shawn.w.foley60
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Comment: C: R DESeq: What exactly is Variance Stabilizating Transformation?
... I'm sure you've found the answer by now, but to take an rlog you can run: `rlogTransformation(cds)` or simply `rlog(cds).` ...
written 5 days ago by shawn.w.foley60
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Answer: A: How do strand specific sequencing protocols work?
... I personally have used two different methods for the generation of strand-specific RNA-seq libraries. 1) We used mutated RNA ligases to directly ligate the adapters onto the RNA before RT-PCR. In this technique we use one enzyme that specifically ligates a DNA adapter to the 3' end of the RNA, and ...
written 12 days ago by shawn.w.foley60
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Answer: A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
... You're correct that technical replicates are not necessary for RNA-seq, however biological replicates are always necessary for statistical analyses. Without replicates you cannot have any p-values. A technical replicate in RNA-seq, in my experience, refers to taking one tube of RNA and then making ...
written 15 days ago by shawn.w.foley60
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Answer: A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
... After more searching I found the answer to my question, I'm posting it here in case someone needs to do a similar analysis in the future. The answer to this question is absent from the crlmm genotyping vignette, however if you look through the full vignette [here][1], you can find the appropriate an ...
written 5 weeks ago by shawn.w.foley60
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How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or crlmm?
... Taking publicly available Affy SNP6.0 data, I am trying to find the normalized signal for each probe. I've used both the "oligo" and "crlmm" from Bioconductor, and these generate a SnpSuperSet variable where I can then use calls(x) to find the genotype (AA=1, AB=2, or BB=3) or I can use confs(x) to ...
bioconductor crlmm snp oligos written 5 weeks ago by shawn.w.foley60
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Comment: C: When performing Fisher's exact test, should I consider all annotated or all dete
... This looks perfect, thank you! ...
written 7 weeks ago by shawn.w.foley60
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When performing Fisher's exact test, should I consider all annotated or all detected transcripts?
... I've performed RNA-seq on 30 cell lines, and am trying to determine if there is an enrichment in oncogenes in genes that are highly expressed (>50 rpkm) across >15 cell lines. Of the ~20,000 annotated mRNAs, there are only ~10,000 mRNAs that are expressed in at least one cell line (rpkm > 1 ...
expression rna-seq fisher's test statistics written 7 weeks ago by shawn.w.foley60 • updated 7 weeks ago by Hussain Ather680
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How do you compare GSEA results between treatments?
... I'm interested in comparing the genes and genes sets regulated by two different drugs. I performed a microarray on Drug A vs control, and Drug B vs control. Using Limma, I calculated the differential expression for all 20,000 genes, and performed a pre-ranked GSEA. I now have ~700 gene sets that are ...
microarray gsea written 9 weeks ago by shawn.w.foley60 • updated 8 weeks ago by Kevin Blighe11k

Latest awards to shawn.w.foley

Scholar 15 days ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
Scholar 5 weeks ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c

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