User: smt8n

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smt8n0
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Posts by smt8n

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gene over-representation analysis with custom background
... Dear all,   I extracted differentially expressed gene from a publicly available data set. I wanted to do an over-representation analysis (OAR) and, since this was an old microarray with less than 10K genes tested, I felt compelled to do OAR against the actual microarray background (also termed ref ...
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Annotation for Mouse Illumina Expression Chip V6.1.1
... Dear all,   I am trying to look at a relatively old mouse data that was taken using Expression Chip v6.1.1. The problem came I when I tried to convert Probe IDs to gene names. Probe IDs are, for example: 10243, 10280, 10575, 20048, ..., 102900072, 102900075, ...   I tried an old keys/mapIds way ...
annotation lumi bead chip mouse probeid2nuid written 16 months ago by smt8n0 • updated 15 months ago by Andy Lynch80
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GAGE package statistical tests
... Dear all,   I am trying to learn the GAGE gene-set enrichment package and apply it to the RNA-Seq data I have. I follow the RNA-Seq workflow: http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf, section 7.1, workflow with DESeq2.   What perplexes me is the b ...
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Comment: C: beadchip annotation data missing gene "names"
... Thank you very much! ...
written 19 months ago by smt8n0
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beadchip annotation data missing gene "names"
... Dear all,   I made an annotation table for beadchip data as following (for the symbol as an example): if(version==3) { require(illuminaHumanv3.db) # Use appropriate annotation DB for expression arrays kegg <- illuminaHumanv3PATH geneName <- illuminaHumanv3GE ...
probe to gene id illumina beadchip probe quality written 19 months ago by smt8n0 • updated 19 months ago by James W. MacDonald45k
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Comment: C: Batch effects in limma
... Thank you for noticing the normalization issue. This is a data set from GEO that did not have regular raw files posted. Most of what was posted was normalized. That is what I used and what you saw. After your post I grabbed the only file with non-normalized data that there was, reshaped it using per ...
written 19 months ago by smt8n0
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Comment: C: Batch effects in limma
... I looked at box plots of intensities and at MDS plots. Just in case I am crazy, I am posting them below. Unfortunately, the batch effects seem too pronounced to be figments of my imagination.   ...
written 19 months ago by smt8n0
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Comment: C: Batch effects in limma
... Dear Aaron,   Thank you for the answer. Unfortunately, it brings up a problem. First a quick question: do I understand correctly that you recommend the  design <- model.matrix(~0 + RNAs) approach that will implicitly take care of the batches? Just making sure since I do not know the "one-way l ...
written 19 months ago by smt8n0
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Batch effects in limma
... Dear all, I realize most facets of my question have been discussed here, but I am having hard time pulling all the answers together and generalizing. I have 36 iPSC, 9 primary CM, and 18 biopsy samples. My quality control plots showed batch effects in the data and I added 3 batches to the design m ...
limma batch effect written 19 months ago by smt8n0 • updated 19 months ago by Aaron Lun17k
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Strange problem with BeadArrayUseCases vignette
... Hi all, I encountered a strange problem running the "Analysis of public data using GEO" part of the code from the BeadArrayUseCases vignette: library(GEOquery) library(limma) library(illuminaHumanv1.db) url <- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE5350/" ...
beadarrayusecases written 20 months ago by smt8n0

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