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Subramanian Karthikeyan ▴ 60

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ADD COMMENT • link updated 20.5 years ago by singaram muthu ▴ 10 • written 20.6 years ago by Subramanian Karthikeyan ▴ 60

score 0 · Answer 1 · 2003-11-17

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Duhaime Johanne ▴ 100

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Johanne [[alternative HTML version deleted]]

ADD COMMENT • link 20.5 years ago Duhaime Johanne ▴ 100

score 0 · Answer 2 · 2003-11-20

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zhao luo ▴ 70

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Hi, I would like to flag bad spots, but I'm not sure what's the criteria for 'BAD'. Please give me some advice Thanks a lots zhao

ADD COMMENT • link 20.5 years ago zhao luo ▴ 70

score 0 · Answer 3 · 2003-11-22

Hello, In our Lab we are starting to run microarray analysis by using the mArray package. We followed the 'Biologists guide to using Bioconductor' published Nov 2002 by C. Bye: http://www.people.fas.harvard.edu/~grosu/downloads/bioconductor_manual .pdf Following the instructions we modified the gal file introducing a column "controls" to specify the blanks and N/A spots. To vizualize these controls in MA plots we try this R code (as indicated in the guide): blanks<-maText(subset=maControls(christian.raw[,1]) == "EMPTY") , labels="o", col="purple") maPlot(christian.raw[,1], text.func = blanks) We tried to exchange "EMPTY" by any control specified and even tried "Control" In any case this resulted in a "syntax error" We crosschecked whether these controls are accesible with the following code: maImage(christian.raw[,1], x="maControls) There we get a warning message and no plot. Here is an extract of our modified gal file. To our knowledge this should be ok. Block Row Column ID Name Controls 4 21 5 H200021155 Homo sapiens cDNA FLJ30327 fis OK 4 21 7 H200021179 Homo sapiens cDNA FLJ32985 fi OK 4 21 8 H200021185 Homo sapiens cDNA FLJ30893 fis OK 4 21 9 n/a n/a NA 4 21 16 n/a n/a NA 4 22 3 Blank Blank EMPTY 4 22 5 Blank Blank EMPTY Does anybody know how to handle this operation (visualization of control spots specified in the gal file) or if we made some other mistake? Thanks (in advance) for help, Christian Riedel Ph.D. student

score 0 · Answer 4 · 2003-11-25

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singaram muthu ▴ 10

@singaram-muthu-543

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Hi, Need your help in the following: I am interedted in the software package - affy (developmental). I have downloaded also. I Requrest you that how to run the package. There is no set up/exe file. I shall be very much grateful if you could kindly help in instructing me that how to use this software package. Thanks & Regards Muthu, S _________________________________________________________________ Garfield on your mobile. Download now. http://server1.msn.co.in/sp03/gprs/ How cool can life get?

ADD COMMENT • link 20.5 years ago singaram muthu ▴ 10

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> I am interedted in the software package - affy (developmental). I have > downloaded also. I Requrest you that how to run the package. There is no > set up/exe file. Do you have R? You might want to read, if you haven't already, the section in the FAQ: http://www.bioconductor.org/faq.html#How%20can%20Bioconductor%20be%20o btained This explains how to get R running (if you aren't yet), and how to get the Bioconductor packages running in R. > I shall be very much grateful if you could kindly help in instructing me > that how to use this software package. For this, you should go to the "Vignettes" page and look at the ones pertaining to the affy package. -J

ADD REPLY • link 20.5 years ago Jeff Gentry ★ 3.9k

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> Hi, > > Need your help in the following: > > I am interedted in the software package - affy (developmental). I have > downloaded also. I Requrest you that how to run the package. There is no > set up/exe file. > > I shall be very much grateful if you could kindly help in instructing me > that how to use this software package. > > Thanks & Regards > Muthu, S affy is not standalone software. you need to run it as an R package. you can retrieve R from cran.r-project.org. get that installed and get a little familiar with it. the affy package can be installed in your version of R by running some commands inside R, once you have it installed. source("http://www.bioconductor.org/getBioC.R") getBioC("affy", rel="devel") will start the installation process, as long as you have sufficient web connectivity. find the vignettes for affy on the web page under Documentation.

ADD REPLY • link 20.5 years ago Vincent J. Carey, Jr. 6.7k