User: adam_pgsql

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adam_pgsql70
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9 years, 4 months ago
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9 years, 8 months ago
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Posts by adam_pgsql

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Comment: C: Tiling array analysis, ACME problem
... On 1 Jun 2010, at 14:55, Sean Davis wrote: > > > On Tue, Jun 1, 2010 at 9:11 AM, adam_pgsql wrote: > > Hi, > > I am looking for modules that can analyse overlapping tiling arrays (Agilent) used for expression studies. In testing ACME, the example in the documentation fails wi ...
written 9.4 years ago by adam_pgsql70
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Tiling array analysis, ACME problem
... Hi, I am looking for modules that can analyse overlapping tiling arrays (Agilent) used for expression studies. In testing ACME, the example in the documentation fails with this error: [R 2.10.1, OSX 10.6.3] > library(ACME) > samps <- data.frame(SampleID = 1:3, Sample = paste("Sample", 1 ...
annotation acme written 9.4 years ago by adam_pgsql70 • updated 9.4 years ago by Sean Davis21k
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Colouring limma MA plot
... I am trying to colour a limma generated MA plot by fold change. I can do it this way: status <- bugs.colour(RG,1) attr(status,"values") <- c("nonsignificant", "present", "absent", "Blank", "Buffer", "ACTB", "GAPDH", "Positive") attr(status,"col") <- c("black", "red", "green", "black", "br ...
limma written 9.5 years ago by adam_pgsql70 • updated 9.5 years ago by Wolfgang Huber13k
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Comment: C: CGH analysis without genome positions
... On 7 Apr 2010, at 00:01, Sean Davis wrote: > On Tue, Apr 6, 2010 at 6:53 PM, adam_pgsql wrote: >> >> On 6 Apr 2010, at 19:15, Sean Davis wrote: >> >>> On Tue, Apr 6, 2010 at 1:58 PM, Sean Davis wrote: >>>> On Tue, Apr 6, 2010 at 1:47 PM, adam_pgsql wrot ...
written 9.5 years ago by adam_pgsql70
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Comment: C: CGH analysis without genome positions
... On 6 Apr 2010, at 19:15, Sean Davis wrote: > On Tue, Apr 6, 2010 at 1:58 PM, Sean Davis wrote: >> On Tue, Apr 6, 2010 at 1:47 PM, adam_pgsql wrote: >>> >>> Hi, >>> >>> I am trying to do some CGH analysis with Agilent arrays, but all the analyses metho ...
written 9.5 years ago by adam_pgsql70
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CGH analysis without genome positions
... Hi, I am trying to do some CGH analysis with Agilent arrays, but all the analyses methods seem to require genome position information. Does anyone know of any packages that will call genes as present/absent without the genome position? thanks for any help adam ...
cgh written 9.5 years ago by adam_pgsql70 • updated 9.5 years ago by Sean Davis21k
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Calling genes present or absent in CGH data
... Hi, I have a CGH data set (two colour spotted array data) where i have performed various filtering and normalisation steps using LIMMA. I now have a matrix of log ratios and was wondering which are people's preferred functions or tools to call genes as present or absent? thanks for any advice Ada ...
cgh limma written 9.7 years ago by adam_pgsql70 • updated 9.7 years ago by Sean Davis21k

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