User: michaelsbreen1

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Location:
University of Southampton
Last seen:
6 years, 7 months ago
Joined:
8 years, 2 months ago
Email:
m*************@gmail.com

I am a bioinformatician with broad interests in fundamental molecular evolution and biomedical research. Currently, I use just about any data I can get my hands on which can be translated into biomedical research.

Posts by michaelsbreen1

<prev • 9 results • page 1 of 1 • next >
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Whole Blood Gene Expression Deconvolution
... Hi all, We routinely work with gene-expression data sets generated from whole-blood of subjects of case and control status. Recently, there seems to be quite an interest in deconvolving cell-type specific gene-expression signatures from whole blood and we too think this is an interesting concept. ...
expression written 6.7 years ago by michaelsbreen180
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Comment: C: Rna-Seq And Microarray Classification
... Cheers guys. I'll meditate a bit on these approaches and test them out. I still think it is quite surprising though that still you can not take a classifier from one study and put it on to another, using expression, to see how it performs. ...
written 7.1 years ago by michaelsbreen180
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Comment: C: Rna-Seq And Microarray Classification
... Thanks. Although, I wouldn't want to normalize the both them. It's my impression that in order to make the two distributions somewhat similar, RNASeq needs to be variance stabilise transformed and a covariate shift needs to be used in order to make the two distributions more similar. Although these ...
written 7.1 years ago by michaelsbreen180
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Comment: C: Rna-Seq And Microarray Classification
... Classification with binary gene-expression was an idea. I see it was put out there in 2009 but I was completely unaware of this paper. Cheers, this may provide useful for us. ...
written 7.1 years ago by michaelsbreen180
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Rna-Seq And Microarray Classification
... Hi All, I am interested in developing a prognostic classifier in the following way: Use a large RNA-Seq cohort with SVM and LOOCV with RFE to develop a prognostic classifier that is able to distinguish between two phenotypes. I want take this classifier and test it on a different Microarray coh ...
rnaseq classification microarray written 7.1 years ago by michaelsbreen180 • updated 7.1 years ago by Charles Warden7.9k
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Answer: A: Annotation Of Probeset-Level Data Of Affymetrix Hugene-1_0-St-V1 Chip
... Hi, A large proportion of these 11363 IDs without annotation are reflective of control probes (~4000 of them). The remaining ~6000 probes without annotation reflect probes with no entrez id annotations. This happens because the probes are designed poorly. From the 32K ProbeIDs it common to fil ...
written 7.5 years ago by michaelsbreen180
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Goseq Error Loading Length Data
... Hi all , I receive an error loading length data with GOSeq. I have count data generated by RSEM counting to hg19. Following I used edgeR to identify DEGs. Now I am interested in using GoSeq for gene ontology of my DEG list. In my code I create a vector and load this into the GoSeq framework. ...
gene R bioconductor hg19 written 7.6 years ago by michaelsbreen180 • updated 7.6 years ago by Alex Reynolds31k
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Pathway Analysis For Paired Microarray Data & Paired Rna-Seq Data?
... Hi All, I am pursuing Pathway Analysis for two different analyses. The first is a paired microarray dataset and the second is an RNA-Seq paired dataset. Many tools available for pathway analysis don't take into consideration paired (matching) data. In the microarray world exist much methodology ...
enrichment microarray rna-seq written 7.6 years ago by michaelsbreen180 • updated 5.7 years ago by dompearcejankowski10
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R: Gene Matrix (.Txt File) To Boxplot And Rle, Nuse Plots
... Hi all, I am analyzing microarray data. I am using a new normalization approach which outputs into a gene matrix text file. Normally I take raw CEL files and use "ReadAffy" function, plot a raw boxplot, normalize with RMA, then plot a normalized boxplot following I write it to a gene matrix, som ...
R microarray written 8.2 years ago by michaelsbreen180 • updated 8.2 years ago by Sean Davis26k

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