User: Pita

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Pita120
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Posts by Pita

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mean vs median of pixel values within spot mask wasRe: something weird with read.maimages and .gpr files
... It seems that I answered my own question .... There was a typo that was entered into the Genepix software so the output would not parse. Limmas read.maimages looks specifically for the F532 Mean for the R channel, instead F594 Mean was written Since it is the case that the Mean of the pixels in th ...
limma trigger written 14.6 years ago by Pita120
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Comment: C: Anyone have a GO slim list for Affy HG-U133A or HG-U133Av2?
... what can trigger the following error? I have imported many genepix files without any problem >> RG.new.gpr <- read.maimages(files.new,"genepix",wt.fun=wtflags(0.1)) >Error in "[.data.frame"(obj, , columns$Gf) : > undefined columns selected This is with limma version 1.8.2 ...
written 14.6 years ago by Pita120
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limma_1.8.21 was: LIMMA - timecourse and direct comparison exp. design
... By the way CRAN seems to only have limma_1.8.16, not sure if someone needed to know that CRAN is not up to date with respect to limma. I downloaded 1.8.21 from Gordon's site. Peter ...
limma written 14.7 years ago by Pita120
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Comment: C: annotation for ath1121501 (?)
... At 08:05 PM 2/7/2005, Matthew Ritchie wrote: >The information from the duplicate spots can be summarised using lmFit() >with the appropriate arguments. The approach taken in limma is to assume >that the duplicate spots are correlated by being on the same array, a >fixed distance apar ...
written 14.7 years ago by Pita120
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Answer: A: annotation for ath1121501 (?)
... I have 3 questions: How are duplicate spots treated when performing the normalizationWithinArrays? Are they treated separately as far as the regression is concerned? How are duplicate spots treated when performing the normalizationBetweenArrays? Are they somehow treated together in the scale norm ...
written 14.7 years ago by Pita120
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Answer: A: latest limma package
... If you do an update or install from CRAN in R you will find the latest, that seems to be where Smyth is placing it. Peter At 02:33 PM 1/26/2005, Nisha Mulakken wrote: >Hi all, > >I just read on http://bioinf.wehi.edu.au/limma/ that >the latest stable version of the limma package is > ...
written 14.7 years ago by Pita120
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Using limma with contrast matrix ,replicate spots,
... What is the significance of this error? What does this tell me about these two samples?. I added the coeficients for the donor then re-calculated the fit. > donor.fit = lmFit(MA, design.III) Coefficients not estimable: HISS0039 HISS0050 The design matrix I used was as follows, you can se ...
written 14.7 years ago by Pita120
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Comment: C: Using limma with contrast matrix ,replicate spots, donor effects
... I am assuming that for the design matrix, I just need to add a column for each donor and plug in the 1's for the appropriate rows to my existing design that specifies the infection type timepoints (A_0,A_6, ... C_42,C_72, Donor1, Donor2, etc ...) ??? Is this correct? Peter At 12:17 AM 1/22/2005 ...
written 14.7 years ago by Pita120
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Comment: C: Using limma with contrast matrix ,replicate spots, donor effects
... At 12:17 AM 1/22/2005, Gordon Smyth wrote: >Having within-array replicate spots on your arrays makes no difference at >all to the design and contrast matrices. (With one exception, which is >that you can't fit a random block effect in limma and estimate a duplicate >spot correlation at t ...
written 14.7 years ago by Pita120
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Using limma with contrast matrix ,replicate spots, donor effects
... Thank you Anne I will look at that example, and try to work things out today. The one thing I dont understand is how to combine creating the correlations for the duplicate spots in the chips with a contrast matrix, or even if I need to? Peter At 11:11 AM 1/20/2005, Arne.Muller@sanofi-aventis.com ...
hiv limma written 14.7 years ago by Pita120 • updated 14.7 years ago by Gordon Smyth38k

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