User: brett.vanderwerff

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Posts by brett.vanderwerff

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Comment: C: Is there a good way to get the proportions of isoforms *within* a condition usin
... I wasn't sure because the isoforms might extract different or have different lengths which would affect the numbers of reads they get vs some other isoform from the get go. I know cross gene comparisons are kind of tricky so I thought I would ask. ...
written 13 months ago by brett.vanderwerff20
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Is there a good way to get the proportions of isoforms *within* a condition using output from kallisto
... I am using kallisto to analyze some RNA-seq samples. So I know that you can get a good idea of the differential expression of isoforms across conditions downstream of kallisto using tools like sleuth and IsoformSwitchAnalyzeR. What I am wondering is if there is method or library for determining the ...
isoforms kallisto rna-seq written 14 months ago by brett.vanderwerff20
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Comment: C: Just looking for some confirmation that this microarray analysis approach is cor
... First, thank you for getting back. The platform of the array is `GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array` I am mostly following this guide: https://wiki.bits.vib.be/index.php/Analyze_your_own_microarray_data_in_R/Bioconductor I am interested in summarizing expression ...
written 14 months ago by brett.vanderwerff20
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Just looking for some confirmation that this microarray analysis approach is correct
... Hi guys, I am looking at affymetrix microarray data from normal and cancer cells that I found on GEO. I want do stats on the expression level of just one gene of interest between normal and cancer cells. I have done some reading and I am just looking for confirmation that my approach is correct. ...
R affy microarray written 14 months ago by brett.vanderwerff20
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Answer: A: A question about how the kegga function or KEGG analysis in general determines s
... I am still interested in understanding how exactly these statistics are calculated, but I can tell now from just playing around with the function that if 5 genes out of 10 total sig DE genes are in my favorite pathway that will be more sig than if 5 genes out of 100 total sig DE geens are in my favo ...
written 15 months ago by brett.vanderwerff20
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A question about how the kegga function or KEGG analysis in general determines significance.
... Hello, Lets say I did an rna-seq experiment experiment with control and drug, I am interested in KEGG pathways that sig. respond to drug. I do KEGG analysis with the `kegga` function (https://tinyurl.com/y7eszpdo) by passing a list of genes sig. affected by drug as the `de` argument, indicating ...
kegga rna-seq kegg edger limma written 15 months ago by brett.vanderwerff20
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Comment: C: How to design qPCR primers to validate RNA-seq experiment?
... Thank you for responding. I have used Primer3, but my question is less about what primer tool to use and more about what transcript for a particular gene I should be designing my primers against. ...
written 18 months ago by brett.vanderwerff20
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Comment: C: How to design qPCR primers to validate RNA-seq experiment?
... Yes I am trying to validate analysis results, I was not sure how much detail was needed, In apologize for that I have updated my questions to better describe my pipeline. ...
written 18 months ago by brett.vanderwerff20
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How to design qPCR primers to validate RNA-seq experiment?
... Hello, I did a bulk mRNA-seq experiment where I treated human cells in vitro with control of drug. I am only interested in determining differential gene expression at the gene level between these groups. I isolated RNA from treated cells and used poly-A selection and did sequencing on the illumina ...
rna-seq qpcr written 18 months ago by brett.vanderwerff20 • updated 18 months ago by Malcolm.Cook1.1k

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