User: kfbargad@ehu.es

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Posts by kfbargad@ehu.es

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Fwd: pmStrand() in oligo (version...)
... Dear list, I am thinking of using RMA to analyse glass-spotted SNP arrays and extract copy number information. I believe "Oligo" package does this for affy chips. Do you think I could use "makePlatformDesign" package to create a custom cdf file for these chips and then use "Oligo" package for perf ...
written 12.4 years ago by kfbargad@ehu.es270
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Comment: C: QC in simpleaffy
... Dear list, sorry for this very basic question but I have searched the R manual without success. What function do I need to randomly split a data.frame into two data.frames (for example a data.frame containing 200 rows and 5 columns into two of say 150 and 50 rows each)? Should I first create a vec ...
written 12.5 years ago by kfbargad@ehu.es270
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Answer: A: LIMMA makeContrasts question
... Dear TS, I am a biologist and found "Design and Analysis of Experiments" by DC Montgomery very useful, although it is not a manual on how to make contrasts HTH David > Dear TS, > > You are wanting to select genes which satisfy several conditions. > There is no way to do this with a ...
written 12.9 years ago by kfbargad@ehu.es270
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Comment: C: median of the NUSE value
... Dear Ben and list, I have just rerun my code and now it works fine. Sorry for bothering, there was probably some typo. Regards, David > Below is my results using affyPLM 1.9.5. No particular problem here > with that version. What was your fitPLM call? > > > > > > > &g ...
written 13.3 years ago by kfbargad@ehu.es270
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median of the NUSE value
... Dear list, I am using affyPLM for my QC, and am trying to obtain the median of the NUSE values for my chips. if I type >NUSE(Pset, main = "NUSE values") I get the NUSE boxplot but if I type > NUSE(Pset, type = "stats") Error in match.arg(type) : 'arg' should be one of plot, values or > N ...
cdf affy gcrma affyplm affyio written 13.3 years ago by kfbargad@ehu.es270 • updated 13.3 years ago by Ben Bolstad1.2k
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Answer: A: limma: get all sig genes from multiple contrasts
... If I am not wrong, section 8.6 of the limma manual explains what you want, and that is fit2$F.p.value hth, David > I realize this may be a silly question, but I have gone through all the > case studies in the limma users manual and I can't seem to find the > answer to this anywhere. I ...
written 13.4 years ago by kfbargad@ehu.es270
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error creating new exprSet
... Dear list, I tried to create a new exprSet from my filtered Affy genelist using R 2.3.0 with affy "1.10.0" simpleaffy "2.6.0" genefilter "1.10.0" and I got the folowing error: good.eset = new("exprSet", exprs = good) Error in validObject(.Object) : invalid class "exprSet" object: number of exprs ...
affy written 13.4 years ago by kfbargad@ehu.es270 • updated 13.3 years ago by Seth Falcon7.4k
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day-of-hybridisation variability
... Dear list, does anyone know of any studies performed to quantify variability due to day of hybridisation of affy chips? we had an experiment where we had 12 conditions and three replicates per condition and due to lab reasons, we had to hybridise on three different days, as follows: rep1 for each ...
affy written 13.4 years ago by kfbargad@ehu.es270 • updated 13.4 years ago by martin.schumacher@novartis.com80
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a thin hibridisation line
... Dear list, has anyone noticed that there is a thin horizontal line across the whole array with different intensity about two thirds down the array, visible when looking at the pseudoimages generated using residuals in affyPLM? I have seen this line in quite a few of our arrays, even different speci ...
written 13.4 years ago by kfbargad@ehu.es270
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Answer: A: Analysis of RT-PCR data
... Dear list, I have three groups of samples (Tto, NoTto, C) and have made the three possible pairwise contrasts as follows: design.tto <- model.matrix(~-1+factor(c (1,1,2,2,2,3,2,1,3,1,2,2,3,1,1,2,1,1,3,1))) colnames(design.tto) <- c("C","Tto", "NoTto") fit.tto <- lmFit(eset,design.tto) co ...
written 13.4 years ago by kfbargad@ehu.es270

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