User: hs.lansdell

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hs.lansdell10
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Posts by hs.lansdell

<prev • 21 results • page 2 of 3 • next >
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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 11 months 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 11 months ago by hs.lansdell10 • updated 11 months ago by Gavin Kelly560
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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 11 months 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 11 months ago by hs.lansdell10 • updated 11 months ago by Michael Love19k
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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 11 months 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 11 months 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 12 months ago by hs.lansdell10
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Comment: C: Tximport with RSEM error
... I was trying to run the vignette code just to make sure I formatted my own files correctly. I want to run my own genes.results files. I'm trying to determine if a sample.txt file is needed for that as it states here: RSEM sample.genes.results files can be imported by setting type to "rsem". files ...
written 12 months ago by hs.lansdell10
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Comment: C: Tximport with RSEM error
... Which I understand and have done, what I'm trying to understand now is what the sample.txt file should look like.  ...
written 12 months ago by hs.lansdell10
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Comment: C: Tximport with RSEM error
... Thanks for yours thoughts, I started just at the RSEM section and missed the making of the vector. It would be helpful to see the example inputs, so I tried running the vignette examples, but I cannot locate the 'extdata' anywhere within the package. When I run the command: dir <- system.file(" ...
written 12 months ago by hs.lansdell10

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