User: Nathan Haigh

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Nathan Haigh120
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Posts by Nathan Haigh

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Comment: C: bovine Annotation package(s)
... Hi Louisa, Just to clarify with a few things I've learnt in the last week or two regarding the Bioconductor annotation packages/framework. There are currently two types of annotation packages: 1) Those built by AnnBuilder 2) Those built by SQLForge The former are the older style annotation packag ...
written 11.2 years ago by Nathan Haigh120
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Help with lm and predict
... I'm trying to predict some values given a linear model. And I'm pulling my hair out trying to get it to work! I have a data file (several rows shown here): -- start data file -- Mean M/Z SD M/Z N Mean Int (Log) SD Int (Log) 59.99434 0.004952 100 7.5543 0.3918 67.952 ...
assign written 12.2 years ago by Nathan Haigh120
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Comment: C: limma - Considering Batch Effect
... James MacDonald wrote: > Hi Nathan, > > > Nathan Haigh wrote: >> I know this topic has arisen a few times from searching the mail >> archive, but I'm still not clear on what/how to do this. >> >> Here is my experimental setup: >> Array Param1 Param2 R ...
written 12.2 years ago by Nathan Haigh120
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Comment: C: Saving Median values to an Affy CEL file
... Seth Falcon wrote: > Nathan Haigh writes: > >> I'm on a Debian machine, running the latest "stable" R version according >> to Debian. I can try installing 2.5.1 from unstable if you think that's >> gonna be required. I'll let you know if it's gonna cause problems with >&g ...
written 12.2 years ago by Nathan Haigh120
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Comment: C: Saving Median values to an Affy CEL file
... Seth Falcon wrote: > Nathan Haigh writes: > > >> James MacDonald wrote: >> >>> Hi Nathan, >>> >>> What's your sessionInfo()? >>> >>> sessionInfo() >>> >> R version 2.4.0 Patched (2006-11-25 r39997) >> i486-pc-lin ...
written 12.2 years ago by Nathan Haigh120
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Comment: C: Saving Median values to an Affy CEL file
... James MacDonald wrote: > Hi Nathan, > > What's your sessionInfo()? > sessionInfo() R version 2.4.0 Patched (2006-11-25 r39997) i486-pc-linux-gnu locale: LC_CTYPE=en_GB;LC_NUMERIC=C;LC_TIME=en_GB;LC_COLLATE=en_GB;LC_MONETARY =en_GB;LC_MESSAGES=en_GB;LC_PAPER=en_GB;LC_NAME=C;LC_ADDRESS=C ...
written 12.2 years ago by Nathan Haigh120
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limma - Considering Batch Effect
... I know this topic has arisen a few times from searching the mail archive, but I'm still not clear on what/how to do this. Here is my experimental setup: Array Param1 Param2 Rep Batch 1 H 4 1 1 2 H 4 2 2 3 H 4 3 2 4 ...
limma genespring written 12.2 years ago by Nathan Haigh120 • updated 12.2 years ago by James W. MacDonald51k
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Comment: C: Saving Median values to an Affy CEL file
... James W. MacDonald wrote: > Hi Nathan, > > Nathan Haigh wrote: >> I have a need to calculate the median of probes across 4 reps and save >> these medians to a single Affy ATH1 CEL file. Can this be done with >> bioconductor? >> > > I believe so. See the affxpar ...
written 12.2 years ago by Nathan Haigh120
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Comment: C: Using a custom CDF file
... James W. MacDonald wrote: > Hi Nathan, > > Nathan Haigh wrote: >> I'm using the xspecies [1] approach of hybridising gDNA to the Affy ATH1 >> chip. Using these, one masks out low intensity probes and creates a new >> CDF file - this is done several times using a different ...
written 12.2 years ago by Nathan Haigh120
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Using a custom CDF file
... I'm using the xspecies [1] approach of hybridising gDNA to the Affy ATH1 chip. Using these, one masks out low intensity probes and creates a new CDF file - this is done several times using a different intensity threshold. I then want to analyse RNA hybs to the ATH1 chip using each of these different ...
cdf written 12.2 years ago by Nathan Haigh120 • updated 12.2 years ago by James W. MacDonald51k

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Popular Question 11.2 years ago, created a question with more than 1,000 views. For Using a custom CDF file

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