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User: shawn.w.foley

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shawn.w.foley • 140
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Posts by shawn.w.foley

<prev • 19 results • page 1 of 2 • next >
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Answer: A: Venn diagram generation criteria from RNAseq data
... It depends on the exact question that you're trying to address, but I'd argue that both approaches are useful. I would generate a 3-way Venn diagram for all genes that pass the differential expression cutoff (FDR < 0.05, or whatever cutoffs you apply), that will tell you how similar the samples A ...
written 5 days ago by shawn.w.foley • 140
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Comment: C: miRNA mRNA interaction studies
... I think we need a bit more information about your project and your goals. 1) What are the samples? Drug treated? Mutant vs Wildtype? miRNA upregulation? 2) Is this some sort of miRNA-seq or mRNA-seq? Are you up/downregulating an miRNA then seeing which genes are differentially expressed? 3) Is the g ...
written 6 days ago by shawn.w.foley • 140
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Comment: C: General Question to shRNA-Seq analysis
... DESeq2 is very similar to EdgeR, and their tutorial has a very nice walk through of multi-factor designs, including common errors and how to address them. It's worth a read, and if you aren't married to EdgeR, I found DESeq2 to be more user friendly when I was starting out: http://bioconductor.org ...
written 25 days ago by shawn.w.foley • 140
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Comment: C: Extract rows from file two having the 4th column ( which contain /1 /2 signs ) i
... The error from the python code, `printList.append(lineList[6]) #Append your tag to printList IndexError: list index out of range` indicates that the script reaches a line where there are not seven columns in you file. Is this a typo in the file? And I'm not sure why you're having an issue with the ...
written 28 days ago by shawn.w.foley • 140
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Comment: C: Extract rows from file two having the 4th column ( which contain /1 /2 signs ) i
... Apologies, I edited the above code. The tag name is in column 5 of the file2, the original code assumed it was in column 4. I also added a line in the python script to remove the header from file2. ...
written 4 weeks ago by shawn.w.foley • 140
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Answer: A: Extract rows from file two having the 4th column ( which contain /1 /2 signs ) i
... You can do this pretty easily in python, you'll read through File 1 and save the 7th column in a list. Then read through File 2, delimit the 5th column on the slash ("/") and if the element before the slash is in your list then print the line. Example code would be: inFile1 = open('file1','r') ...
written 4 weeks ago by shawn.w.foley • 140
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Answer: A: GSEA, input metrics
... To perform GSEA analysis we typically use the log2-fold change **NOT THE ABSOLUTE FOLD CHANGE** with a pre-ranked GSEA. Pre-ranked GSEA will give you an output for enriched genes in the positive direction (upregulated) and enriched genes in the negative direction (downregulated). By using the absolu ...
written 3 months ago by shawn.w.foley • 140
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ChIP-seq differential binding with multiple replicates using MACS2 bdgdiff.
... Hello, I'm trying to perform a differential binding ChIP-seq experiment and am struggling with the best way to incorporate my replicates using MACS2. I have two sets of samples, control rep 1-3 and control input, as well as treated rep 1-3 and treated input. If I run macs2 callpeak as recommended I ...
bdgdiff macs2 chip-seq written 8 months ago by shawn.w.foley • 140
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Comment: C: Analyzing RNA-seq without replicates
... Thank you for the help, this input has been great! DESeq2 will also allow me to calculate the expression fold changes for each individual patient pre- and post-treatment. I want to confirm that I should not put any weight into the reported p-values/FDRs for the individual patients. Instead I shoul ...
written 10 months ago by shawn.w.foley • 140
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Analyzing RNA-seq without replicates
... Hello, I'm currently analyzing an RNA-seq experiment consisting of clinical patient samples pre- and post-treatment, for individuals that had no response (NR, n=6), partial response (PR, n=4), or complete response (CR, n=2) to our compound. Unfortunately, no replicates were collected for each indiv ...
cufflinks isoem2 deseq2 isode2 rna-seq written 10 months ago by shawn.w.foley • 140 • updated 10 months ago by i.sudbery • 2.8k

Latest awards to shawn.w.foley

Popular Question 28 days ago, created a question with more than 1,000 views. For Analyzing RNA-seq without replicates
Scholar 28 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
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Analyzing RNA-seq without replicates
Scholar 11 months 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 11 months ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
Scholar 11 months 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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