Question: newbie question: how do I get affy annotations
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gravatar for Hao Liu
15.6 years ago by
Hao Liu130
Hao Liu130 wrote:
Dear All: can someone teach me how to get affy libraries into R? I just tried library(hu6800) and I doubt if there are any other libraries there. Best regards Hao Liu, Ph. D
affy • 521 views
ADD COMMENTlink modified 15.6 years ago by John Zhang2.9k • written 15.6 years ago by Hao Liu130
Answer: newbie question: how do I get affy annotations
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gravatar for Anna Cao
15.6 years ago by
Anna Cao90
Anna Cao90 wrote:
Hi, I'm trying to plot a vector of log ratios using the imageplot functions but it keeps telling me my dimensions are incorrect. Here's what I did. x <- dir(pattern="test.txt") # where test.txt contains a 16200 by 12 matrix of numbers (with NAs) x <- read.delim(x, header=TRUE) y <- c(x[1]) imageplot(y,layout=list(ngrid.r=5,ngrid.c=12,nspot.r=30,nspot.c=9)) And this is the error message: Error in imageplot(y, layout = list(ngrid.r = 5, ngrid.c = 12, nspot.r = 30, : Number of image spots does not agree with layout dimensions I check the dimension of y and it's indeed 16200. > dim(data.frame(y)) [1] 16200 1 What am I doing wrong? Thanks!! Anna
ADD COMMENTlink written 15.6 years ago by Anna Cao90
> Hi, > > I'm trying to plot a vector of log ratios using the imageplot functions > but it keeps telling me my dimensions are incorrect. > > Here's what I did. > > x <- dir(pattern="test.txt") > # where test.txt contains a 16200 by 12 matrix of numbers (with NAs) x > <- read.delim(x, header=TRUE) > y <- c(x[1]) > imageplot(y,layout=list(ngrid.r=5,ngrid.c=12,nspot.r=30,nspot.c=9)) > > > And this is the error message: > Error in imageplot(y, layout = list(ngrid.r = 5, ngrid.c = 12, nspot.r = > 30, : > Number of image spots does not agree with layout dimensions > > > I check the dimension of y and it's indeed 16200. >> dim(data.frame(y)) > [1] 16200 1 > > What am I doing wrong? If you look at the help page for 'imageplot', you'll see that the first argument is expected to be a "numeric vector or array". You're giving it a list, as you could check for yourself by typing 'class(y)'. Your object 'y' doesn't have any dimensions and has length 1, which you'd see if you typed 'dim(y)'. All would work fine if you extracted 'y' from 'x' using 'y <- x[,1]' or converted 'y' to numeric using 'y <- as.numeric(y)'. Gordon > Thanks!! > > Anna
ADD REPLYlink written 15.6 years ago by Gordon Smyth38k
Answer: newbie question: how do I get affy annotations
0
gravatar for mai98ftu@studserv.uni-leipzig.de
15.6 years ago by
Go the BioConductor website www.bioconductor.org) and click on "Software: How To" to get general information on how to install BioConductor packages. Then click on "MetaData". There you will find dozens of annotation packages to download and install in R. J. Quoting Hao Liu <liuha@umdnj.edu>: > Dear All: > > can someone teach me how to get affy libraries into R? I just tried > library(hu6800) > > and I doubt if there are any other libraries there. > > > Best regards > > Hao Liu, Ph. D > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink written 15.6 years ago by mai98ftu@studserv.uni-leipzig.de140
Answer: newbie question: how do I get affy annotations
0
gravatar for John Zhang
15.6 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>can someone teach me how to get affy libraries into R? I just tried >library(hu6800) Bioconductor's MetaData section contains a list of annotation libraries for affy chips. To get a annotation library(e.g. hgu95av2), you may try: > library("reposTools") > install.packages2("hgu95av2") > library("hgu95av2") > >and I doubt if there are any other libraries there. > > >Best regards > >Hao Liu, Ph. D > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 15.6 years ago by John Zhang2.9k
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