User: Eleni Christodoulou

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150
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Location:
Singapore
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2 months, 1 week ago
Joined:
10 years, 10 months ago
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Posts by Eleni Christodoulou

<prev • 64 results • page 1 of 7 • next >
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Comment: C: DESerq2 older releases
... Thank you very much, Michael. For the moment, I don't want to recreate the old results, just check what were the default parameters back then. I was using v1.16.1. Thank you for directing me to the NEWS page of DESeq2 Github; It covers my question.   ...
written 12 weeks ago by Eleni Christodoulou150
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DESerq2 older releases
... Dear Bioc Team, I have been using DESeq2 for my analysis for the past one year or so. In the meanwhile, I have updated my R and Bioconductor, and I have been using different DESeq2 versions. I would like to go to my old results and see again what were the default options of the DESeq, results and l ...
deseq2 release written 12 weeks ago by Eleni Christodoulou150 • updated 12 weeks ago by Michael Love20k
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Comment: C: duplicateCorrelation and Pearson Correlation
... Hello, Aaron and apology for the late reply. Thank you for your response. Yes, there is a batch effect which is evident with MDS. I will then apply duplicateCorrelation in my second problem. Best, Eleni ...
written 2.1 years ago by Eleni Christodoulou150
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Comment: C: duplicateCorrelation and Pearson Correlation
... Dear Aaron, I tried avearrays() for a problem similar to the above. I then want to do differential gene detection using limma. The problem is that some of the replicates are in different batches. I thus want to add the batch in my design matrix. Is this possible when the averaged replicates are acr ...
written 2.1 years ago by Eleni Christodoulou150
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Answer: A: How to get probe names for raw intensity values?
... Hello, I am not working with Affy Arrays but with Illumina. I guess the same things exist for both cases, though. For illumina, there is a manifest file for each array, which maps the  rownames of the array to symbols, entrez_ids etc. One of the manifest's columns is called 'array_address_id'. This ...
written 2.1 years ago by Eleni Christodoulou150
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Comment: C: duplicateCorrelation and Pearson Correlation
... Thank you very much!   ...
written 2.1 years ago by Eleni Christodoulou150
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Comment: C: duplicateCorrelation and Pearson Correlation
... Thank you, Aaron, for the nice illustration of the differences between the methods! Really insightful! At the end, do you maybe mean aveArrays() and not avereps()? My aim is to average the technical replicates of the samples. I also have another case with just a pair of samples: One before and one ...
written 2.2 years ago by Eleni Christodoulou150
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duplicateCorrelation and Pearson Correlation
... Dear BioC people, I am analyzing a wet lab experiment on a cell line with 5 biological replicates. Each biological replicate has 3 or 4 technical replicates. Here is my targets$BiolRep entry targets$BiolRep [1] 1 2 2 1 2 1 4 4 1 4 3 3 3 5 5 5 Some of the biological replicates are sensitive and ...
limma duplicatecorrelation written 2.2 years ago by Eleni Christodoulou150 • updated 2.2 years ago by Aaron Lun21k
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Answer: A: Batch effect removal
... That simple :) Thank you very much! ...
written 2.5 years ago by Eleni Christodoulou150
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Batch effect removal
... Dear BioC community, I am analyzing microarray data from three different batches. There are many technical and biological replicates in the batches. In the past, when I had only two batches, I was using removeBatchEffect function from limma, giving the batch of each sample as argument (with batch=. ...
microarray limma removebatcheffect() written 2.5 years ago by Eleni Christodoulou150

Latest awards to Eleni Christodoulou

Popular Question 17 months ago, created a question with more than 1,000 views. For help with linear model
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Popular Question 23 months ago, created a question with more than 1,000 views. For help with linear model
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Popular Question 23 months ago, created a question with more than 1,000 views. For Significance Analysis of Microarrays (SAM)

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