User: hs.lansdell

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hs.lansdell10
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Posts by hs.lansdell

<prev • 14 results • page 1 of 2 • next >
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Running DESeq2 on top variable genes?
... Since looking at the row variance and DESeq2 both act as ranking mechanisms for genes, is there any sense to taking the top 1000 or 5000 genes with the highest variance across samples from an RNA sequenced set and running the DESeq2 pipeline on that subset to look for differential genes between grou ...
deseq2 genes variance written 1 day ago by hs.lansdell10 • updated 1 day ago by Michael Love15k
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Comment: C: Design model for DESeq2 analysis
... Thank you! I'm trying this now!   ...
written 15 days ago by hs.lansdell10
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Comment: C: Design model for DESeq2 analysis
... Thanks for the input! ...
written 15 days ago by hs.lansdell10
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Comment: C: Design model for DESeq2 analysis
... Sorry! It's a dichotomous outcome. So there's only yes or no. It's a calculated binary outcome based on reported pain 6 weeks out from an event. i.e, over a 7, gets a yes, under gets a no.  Here's all my code:  library(DESeq2) data<-read.csv("TotalRNA.csv", header=TRUE, row.names = 1, strings ...
written 15 days ago by hs.lansdell10
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Design model for DESeq2 analysis
... Hello!  I'm trying to figure out which design model is correct for my human RNA seq data. I have outcome data, here 'condition' that when examined alone, returns no differentially expressed genes (as design=~condition). So digging around led me to believe I need to control for the sex of the sample ...
deseq2 differential gene expression written 16 days ago by hs.lansdell10 • updated 15 days ago by Gavin Kelly510
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Comment: C: DESeq2 output number of genes padj <0.1 is 0?
... So, that was just to show how my files are arranged. My input has 183 samples and 20338 genes.  ...
written 19 days ago by hs.lansdell10
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DESeq2 output number of genes padj <0.1 is 0?
... Morning! I've just run DESeq2 on my RNAseq data with a dichotomous outcome, and I'm getting results that mean I have absolutely no deferentially expressed genes... My input is a count matrix with samples in columns and genes in rows, i.e:               XXX1  XXX2  XXX3 Gene 1 Gene 2 Gene 3 My ...
deseq2 adjusted pvalue written 19 days ago by hs.lansdell10 • updated 19 days ago by Michael Love15k
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Comment: C: results(dds) error: couldn't find results. you should first run DESeq()
... Wow. My bad.  Thank you very much! ...
written 28 days ago by hs.lansdell10
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results(dds) error: couldn't find results. you should first run DESeq()
... Hello! After running DESeq, I attempted to see the results and the following is returned: results(dds) Error in results(dds) : couldn't find results. you should first run DESeq() This is right after successfully (I think) running DESeq.  data<-read.csv("TotalRNA_reads.csv", header=TRUE, r ...
deseq2 error results written 28 days ago by hs.lansdell10
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Comment: C: Tximport with RSEM error
... My files have no column names. From what I can tell my file formats seems to be gene_id some# some# and transcript_id. I reached out to the person who processed the files. Turns out they used rsem v1.1.13.... which has different columns. I'll see if I can import it manually.  Thanks! ...
written 29 days ago by hs.lansdell10

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