User: Iain Gallagher

gravatar for Iain Gallagher
Reputation:
910
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Trusted
Location:
United Kingdom
Last seen:
2 years, 3 months ago
Joined:
9 years, 11 months ago
Email:
i************@btopenworld.com

Posts by Iain Gallagher

<prev • 97 results • page 1 of 10 • next >
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altcdfenvs get wrapCdfEnvAffy error
... Dear List I am trying to customise the cdc file for the Affymetrix mirna20 chip (mirna20cdf). Following the directions in the vignette ‘Modifying existing CDF environments to make alternative CDF environments’ in the altcdfenvs package I have (data_in is from a ReadAffy call): library(altcdfenvs) ...
microarray cdf software error written 2.3 years ago by Iain Gallagher910 • updated 2.3 years ago by James W. MacDonald45k
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Comment: C: PFAM Enrichment in GOstats
... Thanks, I'll check this out today. Think I have used the package in the past anyway. best, iain ...
written 2.5 years ago by Iain Gallagher910
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Comment: C: PFAM Enrichment in GOstats
... Thanks James. I can wait until tomorrow :) best, iain ...
written 2.5 years ago by Iain Gallagher910
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Answer: A: PFAM Enrichment in GOstats
... Hi James (& others) I'm getting the same error with the new Category package. > hgOver <- hyperGTest(params) Error in .testForValidKeytype(x, keytype) : Invalid keytype: PROBEID. Please use the keytypes method to see a listing of valid arguments. > sessionInfo() R version 3.2.0 (20 ...
written 2.5 years ago by Iain Gallagher910
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Comment: C: PFAM Enrichment in GOstats
... Thanks James I'll try again tomorrow. Best, iain ...
written 2.5 years ago by Iain Gallagher910
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PFAM Enrichment in GOstats
... Hello list The GOstats vignette suggests it's possible to test for PFAM category enrichment using a PFAMHyperGParams instance, and indeed I've done this in the past. Today however I'm getting the following error: #make hyperGParams object params<-new("PFAMHyperGParams", geneIds = goiEG, unive ...
gostats category pfam written 2.5 years ago by Iain Gallagher910 • updated 2.5 years ago by Guangchuang Yu800
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biomaRt mapping id RP5-1043L13.1
... Hi List I have a bunch of ids of the form above. What are these ids and what would be the filter option for mappin these to chromosomal coordinates using biomaRt (if it can be done)? Looking on Ensembl, VEGA and Google would suggest that these are clone based VEGA gene ids so I tried querying VEGA ...
biomart vega written 3.5 years ago by Iain Gallagher910 • updated 3.5 years ago by Thomas Maurel700
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xps scheme building
... Hello List I have a set of Rat Gene ST CEL files to analyse and have started looking into using xps for this. I have begun by building the required scheme file for the arrays. I have downloaded the relevant files from affymetrix (RaGene-1_0-st-v1.r4.clf, RaGene-1_0-st-v1.r4.pgf, RaGene- 1_0-st-v1. ...
annotation process xps written 5.4 years ago by Iain Gallagher910 • updated 5.4 years ago by cstrato3.8k
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Answer: A: Best package or code to filter Affymetrix probes by present calls??
... library(affy) dataIn <- ReadAffy() # read in the data rmaData <- rma(dataIn) # normalise and summarise, could also use gcrma etc etc calls <- mas5calls(data) # get PMA calls calls <- exprs(calls) absent <- rowSums(calls == 'A') # how may samples are each gene 'absent' in absent <- ...
written 5.4 years ago by Iain Gallagher910
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Rgraphviz and node label placement
... Hello List Is is possible to place node labels below nodes rather than within them in Rgraphiviz? In the graph below I would like to plot labels below the nodes because many labels are too long to fit within the nodes. library(GO.db) library(GOstats) library(Rgraphviz) GOlist <- c('GO:0031994 ...
go graph written 5.6 years ago by Iain Gallagher910

Latest awards to Iain Gallagher

Popular Question 2.3 years ago, created a question with more than 1,000 views. For extracting sequence from a genome
Popular Question 2.3 years ago, created a question with more than 1,000 views. For pheatmap function is in Which package? - help

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