User: Vegard Nygaard

gravatar for Vegard Nygaard
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Norway
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Joined:
3 years, 11 months ago
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v*************@medisin.uio.no

Posts by Vegard Nygaard

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable e
... My experience is that the "after batch correction"-plots may sometimes be useful and sometimes be very misleading. It all depends on the batch/group balance, what information is used in the correction and what you are looking for. The same would apply for any other effect one tries to remove from th ...
written 4 weeks ago by Vegard Nygaard100
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Answer: A: getGEO error fetching data
... Hi, I suspect there are corrupt files and or bugs in the libraries.   However, I managed to import the data in R without errors by first downloading the two "matrix"-files from here: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE13nnn/GSE13995/matrix/ And then import from file set1 = getGEO(filen ...
written 8 weeks ago by Vegard Nygaard100
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Answer: A: is it possible to before and after batch effect removal from the data and see th
... Hi Amol.   I would argue that in practice it is difficult to remove the batch effect and end up with a completely batch effect free data set. A batch effect removal tool must before removal somehow estimate the batch effect. This estimate has an estimation error, and when the estimate is removed fro ...
written 12 months ago by Vegard Nygaard100
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Answer: A: Method for batch correction
... My colleagues and I spent considerable time looking into problems with attempting to remove the batch effect, which resulted in the article: http://biostatistics.oxfordjournals.org/content/17/1/29 I do not disagree with the other answers from Evan and Aaron. I will explain using somewhat different ...
written 19 months ago by Vegard Nygaard100
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Comment: C: Using of limma moderated t-test with "corrected" expression matrix resulting fr
... It seems that your experimental design takes care of the batch effect. Be aware that this is not only because it is paired, but because all your pairs are inside the same batch (which I am not sure of!). If the two samples had been in different batches, you should have included the batch in limma. ...
written 2.1 years ago by Vegard Nygaard100
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Answer: A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
... Dear Efstathios I see that you have many thoughts and questions regarding the same things my colleagues and I had when working with the article mention in the above referred post: "Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream ...
written 2.1 years ago by Vegard Nygaard100
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Answer: A: Is ComBat introducing a signal where there is none?
... Hi again. I have an update for this post. I did not get any answers. Since the method was widely used, also at our institution, we felt forced to figure this out. Our effort resulted in the recently published article; "Methods that remove batch effects while retaining group differences may lead ...
written 2.2 years ago by Vegard Nygaard100
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Answer: A: To get expression data from GEO
... Hi Jerry. The GSE27597 data set seems to consist of data from two different array platforms, so getGEO returns a list of two ExpressionSet objects. You need to use the list accessor, [[]], to get the individual elements. Something like this: library(GEOquery) data1 = getGEO("GSE27597") datExpr1 = ...
written 3.7 years ago by Vegard Nygaard100
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Is ComBat introducing a signal where there is none?
... Hi bioconductorlist, I am trying to combine microarray data from different experiments(batches) where some of my batches fall completely in one condition (normal/cancer). For this I try to use ComBat in the sva package. After playing around with my data and ComBat it seemed to me that ComBat might ...
microarray clustering cancer limma written 3.9 years ago by Vegard Nygaard100

Latest awards to Vegard Nygaard

Popular Question 11 months ago, created a question with more than 1,000 views. For Is ComBat introducing a signal where there is none?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Is ComBat introducing a signal where there is none?

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