User: wrighth

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wrighth260
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Posts by wrighth

<prev • 26 results • page 1 of 3 • next >
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sva/ComBat with missing values?
... Hi, all; I have a 224-gene OpenArray RT-PCR data set that I'm analyzing, and I strongly suspect one of the runs is having a batch effect on the entire experiment from EDA and analysis of the quality values. Unfortunately, this means that there are a number of missing values in the matrix (though not ...
written 6.2 years ago by wrighth260 • updated 6.2 years ago by Jeff Leek580
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Problem with importing bigWig file from GEO with rtracklayer?
... Hi; I'm using rtracklayer to try to read in a bigWig file from a GEO dataset so I can overlay it on some existing data we have in GenomicRanges objects. Unfortunately, I keep running into the same error: bw <- import(con="GSM1115998_Groseq-MCF7-EtoH- rep2.minusstrand.bigWig", format="bigWig") Er ...
rtracklayer written 6.3 years ago by wrighth260 • updated 6.3 years ago by Dario Strbenac1.5k
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Comment: C: frma for Nimblegen arrays?
... This still seems to be giving me a gene/transcript level summary, however: > pns = probeNames(rat_files_400) > sns = sampleNames(rat_files_400) > pms = pm(rat_files_400) > pms = backgroundCorrect(pms) Background correcting... OK > pms = normalize(pms) Normalizing... OK > colnames( ...
written 7.1 years ago by wrighth260
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frma for Nimblegen arrays?
... Quick (belated) followup question on this: is it possible to get oligo to summarize the probe-level expression rather than the gene level expression? We'd like to try to experiment with some of the other gene-level methods (such as the WGCNA collapseRows, for example) and just see how individual pro ...
microarray annotation normalization affy process safe frma frmatools written 7.1 years ago by wrighth260 • updated 7.1 years ago by Benilton Carvalho4.3k
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Comment: C: frma for Nimblegen arrays?
... Thanks, Benilton; I think I figured it out with buildPDInfoPkgs. However, just to be sure; we were provided an NDF file but I don't think we got a generic XYS file, so I used one of the actual array files for the XYS. It seemed to work alright, but could that be problematic? Hollis Wright, PhD Ojed ...
written 7.1 years ago by wrighth260
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Comment: C: frma for Nimblegen arrays?
... Thanks, Matthew. As a followup, is there no longer an annotation package available for the rat arrays for oligo? I'm getting an error: biocLite("pd.100718.rat.hx12.expr") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s ...
written 7.1 years ago by wrighth260
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frma for Nimblegen arrays?
... Hello, all: two-part question here. We have some expression data from Nimblegen rat arrays that was normalized from our microarray service using the internal RMA process Nimblegen uses in their software. Unfortunately, a few of the arrays had physical defects. We've pulled those from our downstream ...
microarray normalization affy process safe frma written 7.1 years ago by wrighth260 • updated 7.1 years ago by Matthew McCall830
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Old Annotation Packages?
... Hi, all; I've got a large number of expression values that are currently associated with the old 2004 rat genome build RefSeq IDs, and unfortunately it looks like the Ensembl biomaRt and most of the online resources have updated to the new RefSeqs and I can't seem to link back to the old ones. I thi ...
biomart written 7.2 years ago by wrighth260 • updated 7.2 years ago by James W. MacDonald52k
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Answer: A: Cannot construct AnnotationDb for GOStats
... Sorry for double post, hit send accidentally. Basically, any workaround for this other than to pull specific evidence codes? I am stuck on R 2.13 for the moment; tried updating AnnotationDbi via biocLite but no luck. Thanks... Hollis Wright, PhD Ojeda Lab, Division of Neuroscience Oregon Health and ...
written 7.3 years ago by wrighth260
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Cannot construct AnnotationDb for GOStats
... Hi, all; I'm running into some gremlins trying to get together a custom db object to run GOstats on some Affy exon 1.0 data. Specifically, I'm following the instructions in the GOStatsForUnsupportedOrganisms.pdf. We've rolled up expression to Ensembl identifiers, so I've used biomaRt to pull the evi ...
go affy gostats biomart written 7.3 years ago by wrighth260

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