User: rattray56

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rattray560
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Posts by rattray56

<prev • 9 results • page 1 of 1 • next >
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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 27 days ago by rattray560 • updated 27 days ago by Michael Love24k
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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 27 days 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 28 days 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 29 days 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 29 days 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 4 weeks ago by rattray560 • updated 29 days ago by Michael Love24k
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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 5 weeks ago by rattray560 • updated 5 weeks ago by Steve Lianoglou12k
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Comment: A: Comparing various genotypes to a control
... Thankyou, that worked beautifully!   ...
written 14 months ago by rattray560
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Comparing various genotypes to a control
... Hi, I am new to DESeq2 and read through the previous questions, but still not quite sure how to deal with my data.   I have 3 replicates each of 14 different genotypes (each RNA batch made on a different day), and I would like to compare them all to wildtype and each other.  In my summarized experim ...
deseq2 written 14 months ago by rattray560

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