User: Anand C. Patel

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Posts by Anand C. Patel

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problems with lumi
... Dear all, I am having some unusual problems with lumi under R 2.5. I've managed to read in a 30 sample experiment, Mouse6V1 arrays, and perform QC on the experiment. Everything looks OK up to that point. Then lumiT (variance stabilizing transformation) fails. What am I doing wrong? Thanks, Ana ...
microarray normalization lumi written 12.7 years ago by Anand C. Patel100
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Mouse.lumi problems
... Mouse.lumi does not appear to work correctly -- it does not appear to have the Mouse.lumiTARGETID2NUID variable in the environment. Human.lumi does, Mouse.lumi doesn't. Also, for clarification, are either of the new Illumina annotation packages new annotations against more recent genome builds, or ...
annbuilder written 12.8 years ago by Anand C. Patel100 • updated 12.8 years ago by Pan Du1.2k
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Answer: A: problems normalizing in limma
... A quick look at the CSV files generated by PerkinElmer's ScanArray finds a bottom row that only has in it "END DATA". Thus, as Dr. Smyth predicted: > RG2$R[38977,] slide_13295067 slide_13295072 slide_13295071 slide_13295073 slide_13295075 slide_13295079 slide_13295080 slide_13295203 slide_13295 ...
written 14.1 years ago by Anand C. Patel100
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problems normalizing in limma
... I'm having troubles with some new arrays we're working with. After some effort, I've managed to read .csv output from PerkinElmer ScanArray into an RGList object. Warning to anyone else -- the .gpr files this program generates do not conform strictly to the gpr file format, and will make both limm ...
limma written 14.1 years ago by Anand C. Patel100
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430A/B and 430 2.0???
... OK. We have arrays for an experiment that has run over several years. Initial arrays were performed using MG-U74v2 arrays, but we no longer use those data, as we repeated and expanded the experiment later. Currently, we have much data on 430A/B sets: naive mice (3/strain), and two treatment condit ...
normalization limma written 14.3 years ago by Anand C. Patel100
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simpleaffy finds QC problem, now what?
... I have 12 U74Av2 microarrays (and their B and C counterparts). I used SimpleAffy to make an AffyBatch of the raw data from the CEL files, and normalized with MAS5. On plotting QC, I discovered that 3 of the arrays were outliers (see plot attached). Looking at AffyRNADeg, the 3 arrays have a diffe ...
normalization gcrma written 14.6 years ago by Anand C. Patel100
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mouse 430v2 annotation "404" error
... Dutifully having read the old posts before sending a message, I tried to download the developmental metadata package for the mouse430_2 affy genechip like so: install.packages2("mouse4302", develOK=TRUE) I get ultimately: cannot open: HTTP status was '404 Not Found' Where is it? The netaffx annot ...
annotation written 14.7 years ago by Anand C. Patel100 • updated 14.7 years ago by Seth Falcon7.4k
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affylmGUI and annotate problem?
... OK. I have R 2.1 installed. Have "all" of bioconductor installed. Most everything works as expected, excepting that when I try to use affylmGUI, it works (including the GCRMA support, which is great), until the point where the probes are matched to the annotations. At that point I get a string of ...
annotation gcrma written 14.8 years ago by Anand C. Patel100 • updated 14.8 years ago by James W. MacDonald51k
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Problems with MOE430B array metadata (?)
... Although working just fine with the current moe430a annotation file, when I tried to run justGCRMA on a set of moe430b arrays, I get a message about: Error in read.probematrix(filenames = filenames, which = "pm") : End of file reached unexpectedly. Perhaps this file is truncated. I don't understa ...
annotation moe430a moe430b written 15.0 years ago by Anand C. Patel100 • updated 15.0 years ago by James W. MacDonald51k
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analysis post gcrma (factdesign? multtest? siggenes?)
... After much reading, careful work, and success in managing to: 1. load my arrays (moe430a) into bioC 2. get justgcrma to normalize them (windows -- memory limits with gcrma) 3. successfully add pData to them I am now sitting with a set of normalized data. I think (think) I should use factDesign ...
multtest written 15.0 years ago by Anand C. Patel100 • updated 15.0 years ago by James W. MacDonald51k

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