## User: Eleni Christodoulou

Reputation:
150
Status:
Trusted
Location:
Singapore
Last seen:
1 year ago
Joined:
11 years, 8 months ago
Email:
e********@gmail.com

#### Posts by Eleni Christodoulou

<prev • 64 results • page 1 of 7 • next >
1
232
views
1
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 13 months ago by Eleni Christodoulou150
1
232
views
1
... 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 ...
written 13 months ago by Eleni Christodoulou150 • updated 13 months ago by Michael Love25k
1
683
views
1
... 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 2.9 years ago by Eleni Christodoulou150
1
683
views
1
... 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 3.0 years ago by Eleni Christodoulou150
2
424
views
2
... 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 3.0 years ago by Eleni Christodoulou150
1
683
views
1
... Thank you very much!   ...
written 3.0 years ago by Eleni Christodoulou150
1
683
views
1
... 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 3.0 years ago by Eleni Christodoulou150
1
683
views
1
... 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 ...
written 3.0 years ago by Eleni Christodoulou150 • updated 3.0 years ago by Aaron Lun25k
2
545
views
2
... That simple :) Thank you very much! ...
written 3.4 years ago by Eleni Christodoulou150
2
545
views
2
... 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=. ...
written 3.4 years ago by Eleni Christodoulou150

#### Latest awards to Eleni Christodoulou

Popular Question 12 months ago, created a question with more than 1,000 views. For help with linear model
Popular Question 12 months ago, created a question with more than 1,000 views. For GenBank RefSeq conversion
Popular Question 2.3 years ago, created a question with more than 1,000 views. For help with linear model
Popular Question 2.3 years ago, created a question with more than 1,000 views. For GenBank RefSeq conversion
Popular Question 2.7 years ago, created a question with more than 1,000 views. For help with linear model
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Detection p-value: difference between limma and lumi packages
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Significance Analysis of Microarrays (SAM)

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.