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Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
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Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
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Comment: Can I perform a correlation test with 3 biological replicates per condition?
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ATpoint
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> However, even though 3 biological replicates per condition seems to be the norm in these experiments, many papers discuss that we need at…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
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> I have curiosity, why do you make a desing with interceptor and without contrast matrix? Because for a 2-group comparison you do not nee…
Comment: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
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ATpoint
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If you have a one-click workflow ready and the necessary computation power to casually run it, then go for it. If it is any greater effort …
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In my experience integration methods are also often used for different samples/batches across the same technology. The crucial thing is to …
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
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egascon
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Thank you very much! I have repeated the code adding arrayWeights() and it's works! In this case, I have a desing without intercept and c…
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Thank you, I've tried but I see only some appear in the chart in wrong segments. Could you help me to solve this how ? ![enter image desc…
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If the tool mentioned relates to the Perseus application from the Cox lab ([here][1]), it should be free to download after accepting the li…
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
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DGTool
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At least so far to my knowledge, I don't think it would be worth re-mapping to GRCh38.p14, if it is too much trouble or with what you're lo…
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From the marker genes of each cluster, we can determine whether the cluster belongs to human or mouse. Human genes are all capitalized, whi…
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Thanks a lot. It is almost what I need but not all. From your script, I can get information that how much degree different samples contri…
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
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sorry, this isn't a sequence search but search by id ...
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![enter image description here][1]Hi, this is the list/ excel I am uploading ( coverage.xlsx ) ![enter image description here][1] [1…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
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There has been some spam bots in this thread which we cleaned up, you might still get notifications on it, just ignore.
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You're lucky that the senior developer @rob is often around, so you probably get your experts answer soon.
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
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ATpoint
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I think the issue is that there is some contamination of groups. If you plot a PCA or MDS you see that there is a clear separation between …
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