User: sandKings

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sandKings10
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Posts by sandKings

<prev • 14 results • page 1 of 2 • next >
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GSEA Leading edge analysis error
... hi all! I'm trying to run a leading edge analysis on my RNASeq data. Hi everyone! I'm trying to run a leading edge analysis on my RNASeq data using GSEA I first create a ranked gene set file and run GSEA Prerank analysis. I use the GMT file from http://download.baderlab.org/EM_Genesets/curren ...
rnaseq gsea written 12 weeks ago by sandKings10
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Comment: C: Sanger Sequencing showing too much background noise?
... Hi Michael, thanks so much for the feedback. I know she's using nanodrop but am not sure if it's before or after purification. I'll confirm ...
written 12 weeks ago by sandKings10
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Comment: C: Sanger Sequencing showing too much background noise?
... Thanks C. She is using her own oligos and she said she'd make a fresh batch as well as try purifying the DNA. ...
written 12 weeks ago by sandKings10
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Comment: C: Sanger Sequencing showing too much background noise?
... Right! Sorry about that. ...
written 3 months ago by sandKings10
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Sanger Sequencing showing too much background noise?
... One of my colleagues is trying to do Sanger Sequencing. In her words: "I am isolating DNA from tissues, amplifying the gene of interest, purifying it and sending it for sequencing. However, I get high-intensity peaks with lots of background: ![see peaks][1] https://imgur.com/a/R1mwp Do you have ...
sanger sequencing written 3 months ago by sandKings10 • updated 3 months ago by Michael Kosicki80
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Comment: C: Error in ggbiplot
... Thanks, Kevin! Let me try this and see. ...
written 3 months ago by sandKings10
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Error in ggbiplot
... '#plot PCA using all genes require(genefilter) require(calibrate) require(RColorBrewer) library(ggplot2) install.packages("ggfortify") library(ggfortify) pca=prcomp(t(count_matrix)) pc1var <- round(summary(pca)$importance[2,1]*100, digits=1) pc2var <- ro ...
rnaseq rstudio pcaplot written 3 months ago by sandKings10 • updated 3 months ago by Kevin Blighe19k
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Comment: C: Error in my DESeq script
... hahaha! rubber-duck debugging sounds very promising and discreet! Thanks! ...
written 3 months ago by sandKings10
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Comment: C: Error in my DESeq script
... While typing the response to your question, I figured out what I did wrong. The csv file which had my samples and treatments outlined, was for a different cell lineage. I accidentally copied the same file in 2 different folders. So, I didn't have the matching names in the countData. Thanks!! ...
written 3 months ago by sandKings10
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Error in my DESeq script
... Could someone please help me troubleshoot this line? `dds <- DESeqDataSetFromMatrix( countData, DataFrame(condition), ~ condition)` I get the error: Error in if (all(var == var[1])) { : missing value where TRUE/FALSE needed ...
R deseq rna-seq written 3 months ago by sandKings10

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