User: muratcokol

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muratcokol0
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Posts by muratcokol

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Comment: C: Using name parameter in DESeq2-results function
... Awesome. Thanks once again for your help and patience with all the questions. ...
written 11 months ago by muratcokol0
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Comment: C: Using name parameter in DESeq2-results function
... Hi Michael, thank you for this elegant explanation. There is one question I asked above which didn’t get an answer yet, perhaps you could help in this as well - Is it possible to use “contrast” to get the same result as “name”?  ...
written 11 months ago by muratcokol0
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Comment: C: Using name parameter in DESeq2-results function
... My apologies - it is a copy paste mistake. It should have read: newresults <- results(dds, contrast=list("condition1", otherexps)) ...
written 11 months ago by muratcokol0
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Comment: C: Using name parameter in DESeq2-results function
... I had read the ?results page before starting this thread and was unable to find some specifications. In your previous answer, for example, you said that when “name” parameter is called without a comparison, DESeq compares to the “mean” of all samples. As far as I can see, the ?results page does not ...
written 11 months ago by muratcokol0
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Comment: C: Using name parameter in DESeq2-results function
... Hi Michael, if the difference between “name” and “contrast” approaches is the inclusion of X, wouldn’t all results metrics be different? Now some are exactly same, some are exactly double. Also, does this mean I cannot replicate the “name” approach by using “contrast”? Because if I write:  allexps ...
written 11 months ago by muratcokol0
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Comment: A: Using name parameter in DESeq2-results function
... I have a follow-up question on this thread. I implemented the behavior of “name” according to your description as shown below, where I do a contrast of one condition to all other conditions.  expnames <- unique(coldata) expnow <- "1" otherexps <- str_c(“condition”, setdiff(expnames, expnow ...
written 11 months ago by muratcokol0
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Comment: A: Using name parameter in DESeq2-results function
... Hi Michael, thank you very much for your input, it was extremely helpful. ...
written 11 months ago by muratcokol0
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Using name parameter in DESeq2-results function
... Hi. I am trying to make sense of a previously written DESeq analysis which uses the “name” parameter to obtain results. A sample code is below, the first two lines are straightforward - making the Input file and running DESeq. My question is what does the results function return when the name parame ...
rnaseq deseq2 written 11 months ago by muratcokol0

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