User: LilithElina

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LilithElina
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Posts by LilithElina

<prev • 8 results • page 1 of 1 • next >
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Comment: C: DESeq2 results() function
... In the end, we do want to compare all our data. We were just using subsets to figure out the problem. It sounds like there's nothing to be done about the increased computing time compared to the old DESeq, though. Thanks for your help! ...
written 10 weeks ago by LilithElina0
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Comment: C: DESeq2 results() function
... Hi Michael, thanks for your reply! I'm not really sure I understand everything you said, but I gather there's nothing that can be done about the problem. My colleagues did some further testing, using only subsets of the whole 700 sample mess, and learned that it is mostly a problem with specific s ...
written 10 weeks ago by LilithElina0
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DESeq2 results() function
... The DESeq2 package manual states that the results() function "extracts a result table from a DESeq analysis", but I am wondering if the function not only extracts but also generates them. When we extract different comparisons from a huge (400 or more samples) data set, it sometimes takes only a minu ...
deseq2 written 11 weeks ago by LilithElina0 • updated 11 weeks ago by Michael Love15k
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Comment: C: DESeq2 - selective calculation of differential gene expression
... Thank you for your help! ...
written 5 months ago by LilithElina0
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Comment: C: DESeq2 - selective calculation of differential gene expression
... In the example that caused me to ask this question we have no replicates at all, not even for the WT. We did RNA-Seq of ~400 clinical isolates (bacteria, grown in the lab, not ex vivo samples) and we're looking at their general transcription profiles as well as differential expression in comparison ...
written 5 months ago by LilithElina0
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Comment: C: DESeq2 - selective calculation of differential gene expression
... The wild type is also just one sample, apparently, so the conditions df is basically just a df with the sample names as "conditions". ...
written 5 months ago by LilithElina0
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Comment: C: DESeq2 - selective calculation of differential gene expression
... Hey Michael, I'm afraid they're either single or duplicates (depending on the project). We know replicates are important, but with 400 - 500 clinical isolates it just wasn't feasible. So the problem is that we don't really want to compare more than 400 samples against each other. In the old protoco ...
written 5 months ago by LilithElina0
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DESeq2 - selective calculation of differential gene expression
... Hi, due to a strange error in DESeq my group is finally being forced to switch to DESeq2 (probably a good thing). There is one problem we are not sure how to solve, though: In the old DESeq, we would normalise the data and then call nbinomTest() for each comparison we wanted to make. Now, the DESe ...
deseq deseq2 written 5 months ago by LilithElina0 • updated 5 months ago by Michael Love15k

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