User: rattray56

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rattray560
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Posts by rattray56

<prev • 11 results • page 1 of 2 • next >
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Comment: C: How can I delete specific rows (using gene name) from a DESeq2 dataset (or even
... Deleted for now, think I figured it out. ...
written 4 weeks ago by rattray560
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How can I delete specific rows (using gene name) from a DESeq2 dataset (or even just a counts file.
... I am wanting to delete about 9000 rows of genes from 27,000. The rationale is that 20 of our samples are "identical" in the sense that they have all been deleted for an essential gene (permitted due to a drug pretreatment),(aka biological replicates), and the 9000 genes show very strong varia ...
deseq2 written 4 weeks ago by rattray560 • updated 4 weeks ago by Steve Lianoglou12k
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Error in function classes fdef mtable unable to find an inherited method for function assay for signature function missing
... This seems to be a recurrent event for me since I updated DESeq2. The assay function seems not to work anymore. Anyone else had this problem? If so how did you get around it. One on line suggestion was to install R and RStudio from scratch, which I did (took hours), and it didn't solve the probl ...
deseq2 written 3 months ago by rattray560 • updated 3 months ago by Michael Love25k
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Comment: C: How to add row data to DESeqDataSetFromMatrix
... Thanks... I finally figured it out with some local help. Why was my question removed? ...
written 3 months ago by rattray560
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Comment: C: How to add row data to DESeqDataSetFromMatrix
... Not so sure how to do that... help? Here is what I am attempting to do. Also removed column 1 from cts data but I don't think that is the real issue (though advice appreciated!) Step1: import the counts and column data, delete unwanted columns. Import raw count data: cts <- read.table("RawCount ...
written 3 months ago by rattray560
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Comment: C: How to add row data to DESeqDataSetFromMatrix
... I am logged in and have tried to post my code twice now... is there some trick? ...
written 3 months ago by rattray560
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Comment: C: How to add row data to DESeqDataSetFromMatrix
... I am logged in and have tried to post my code twice now... is there some trick? ...
written 3 months ago by rattray560
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How to add row data to DESeqDataSetFromMatrix
... I have a rawcount RNAseq Illumina data set, and a metadata table, but when I try to make a DEseq2DataSetFromMatrix it tells me I have one extra column in my countdata. I do, it is the gene names. How can I get around this. I have tried adding nrow= gene_ID and then just listing the genes, but I d ...
deseq2 written 3 months ago by rattray560 • updated 3 months ago by Michael Love25k
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Using already normalized counts
... I was given an excel spreadsheet with already normalized counts. I cannot seem to get DESeq2 to take data either as HTS counts or DESeq data from matrix. Just not sure how to proceed. ...
deseq2 written 3 months ago by rattray560 • updated 3 months ago by Steve Lianoglou12k
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Comment: A: Comparing various genotypes to a control
... Thankyou, that worked beautifully!   ...
written 16 months ago by rattray560

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