User: Stephen Turner

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Posts by Stephen Turner

<prev • 26 results • page 1 of 3 • next >
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Comment: C: DESeq2 multiple interaction terms 3-factor design
... Also, an older version of the DESeq2 manual has a description of using numeric contrasts, which seems to have completely disappeared from the newer version of the manual. See page 25 here: https://www.bioconductor.org/packages/3.1/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf For standard model matri ...
written 3.9 years ago by Stephen Turner270
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DESeq2 multiple interaction terms 3-factor design
... I have a 3-factor experiment, each factor having two levels: gt: Genotype: XX vs XY sex: Sex: M vs F tmt: Treatment: Letrizole (let) vs Vehicle (veh) I'm interested in the following contrasts: Average main effects of genotype, sex, and treatment across all other levels of other factors In ...
deseq deseq2 interactions multiple factor design written 3.9 years ago by Stephen Turner270 • updated 3.9 years ago by Michael Love26k
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Answer: A: non-BiomaRt die
... I found a bunch of weird characters in my gene names and had the same problems (chicken gene names from Ensembl that had -, /, ., ', and other oddities. Fixed it with a regex.  gene_name <- gene_name[grep("^[A-Za-z0-9]+$", gene_name, perl=TRUE)]   ...
written 4.8 years ago by Stephen Turner270
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Affymetrix HTA 2 array analysis
... Just wondering if anyone has had any luck creating annotation packages for the HTA 2.0 chip? Best, Stephen On Tue, Sep 10, 2013 at 8:24 PM, Mark Cowley wrote: > Hi Vincent & Benilton, > Myself and Philip de Groot have independently tried to create the > pd.hta.2.0.db overnight wit ...
biocviews annotation cancer breast organism process pdinfobuilder written 6.1 years ago by Stephen Turner270 • updated 6.1 years ago by Benilton Carvalho4.3k
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DESeq Normalization Question
... Simon et al., I'm sure this issue has come up before, but I couldn't find an appropriate thread or answer either here or SEQanswers. What feature of the data or the distribution of counts among my samples can cause the sizeFactors to vary much more than the raw counts / library sizes? More detail ...
normalization deseq written 6.6 years ago by Stephen Turner270 • updated 6.6 years ago by Ryan C. Thompson7.4k
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Comment: C: DESeq2 vs limma/voom: PCA completely different. How to proceed?
... Thanks Steve. Using the variance stabilizing transformation on the count data helped very much. The PCA on the variance stabilized data look very similar to the PCA on the limma data. On Tue, Apr 23, 2013 at 2:06 PM, Steve Lianoglou wrote: > Hi Stephen, > > Later on in the DESeq2 (and ori ...
written 6.6 years ago by Stephen Turner270
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DESeq2 vs limma/voom: PCA completely different. How to proceed?
... Short story: I ran a PCA on a matrix of counts from an RNA-seq experiment and then using the voom-tramsformed data, and they're completely different. I imagine my results will be very different using DESeq2 vs limma, and I am wondering how to proceed. Here are the two PCA biplots: http://imgur.com/ ...
limma deseq2 written 6.7 years ago by Stephen Turner270 • updated 6.6 years ago by Simon Anders3.6k
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Comment: C: MEDIPS error extending reads
... Lukas, Thanks for the help and the cautionary note about this design. One more question for you: if I want to test these gene regions in windows (kind of combining the functionality of MEDIPS.meth(..., window_size=500) with a MEDIPSroiSet class, will that window_size argument do what I would expec ...
written 6.7 years ago by Stephen Turner270
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Comment: C: MEDIPS error extending reads
... Lukas, Thanks for the quick response. I went back and mapped my IDs using mm9, and MEDIPS.selectROIs() worked without a problem. However, MEDIPS.createROIset() is what I was looking for - to conduct differential methylation on gene regions of interest. I'm able to create my MEDIPSroiSets, but when ...
written 6.7 years ago by Stephen Turner270
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Comment: C: MEDIPS error extending reads
... Thanks Lukas. That solved that problem. I now have another problem. I'm trying to look at regions of interest as before. After I've called MEDIPS.meth(), I then try to run: dmr_rois <- MEDIPS.selectROIs(results=dmr_all, rois=roi_file, columns=c("counts"), summarize=TRUE) where roi_file is creat ...
written 6.7 years ago by Stephen Turner270

Latest awards to Stephen Turner

Popular Question 16 months ago, created a question with more than 1,000 views. For DESeq2 vs limma/voom: PCA completely different. How to proceed?
Great Question 2.5 years ago, created a question with more than 5,000 views. For DESeq2 vs limma/voom: PCA completely different. How to proceed?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Affymetrix HTA 2 array analysis
Popular Question 2.5 years ago, created a question with more than 1,000 views. For limma topTable with gene symbols in output: annotate problem
Popular Question 2.5 years ago, created a question with more than 1,000 views. For DESeq2 multiple interaction terms 3-factor design
Student 3.9 years ago, asked a question with at least 3 up-votes. For DESeq2 multiple interaction terms 3-factor design
Popular Question 3.9 years ago, created a question with more than 1,000 views. For DESeq2 multiple interaction terms 3-factor design
Popular Question 4.4 years ago, created a question with more than 1,000 views. For DESeq2 vs limma/voom: PCA completely different. How to proceed?

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