[R] R rockie
Help. - Is there a beginner's manual for R? - How do i analyse gene expression data using R, to generate a dendrogram. I would greatlyy appreciate every bit of input. -- BEST Paul [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Clustering In R. (rookie)
Hi all. I have alrge microarray dat set that i would like to analyze using hierarchical clustering. The problem is when i use the command below, > hc<- hclust(dist(array), "ave") i get get this feedback... Error in as.vector(x, mode) : cannot coerce type 'closure' to vector of type 'any' Can some one help me on how i can go about this operation.I am a rookie in R and still learinig to find my way familising with the r environment. Your help will be utmost appreciated. -- BEST Paul = __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plot.hclust with lots of objects
Dear all, The default plotting method for hclust trees looks just fine for few objects like in the example dataset. But when it comes to many features (eg some 1000 and more - I'm trying to visualize clustered microarray data) it renders a tree, that one cannot inspect, because of overlapping text and lines. My question is, is there a way or a plotting parameter for plotting a tree which is wide enough to have all leaves separated and readable labels even for that many objects? This would produce a very big image, so I think scrolling is essential. I believe the answer is simple, but I'm unable to figure it out. Thanks in advance -- BEST Paul Murima __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] HELP ON SCALING GENE EXPRESSION DATA TO -1,0,1
Hello R-Community,
I am a rookie in R and I am fascinated with the power of bio computing
by R. I am analysing gene expression data from Real time PCR. I have
used absolute gene quantitation to measure gene copy number in all my
transcripts. All my data has been normalised them to a housekeeping
gene, which is constitutive expressed.
My problem is as follows.
After normalising some of the genes (which are feature vectors in my
matrix of 26 treatment conditions) are up regulated to over 50 fold.
Now, when plot my heatmap.2 of the matrix, almost everything shows up
as red, in a green-red colour scale.
i.e. from -1,0,1. Is there a way to scale all the data on the matrix
such that when i plot it on a heat map it it reflecting the relative
expression of of each feature, against the treatment condition without
being fixed to the -1, to 1 scale.
Below is how the code i used.
library(gplots)
zcz<- read.table("chitekete.csv", header = T, row.names=1, sep=",");
xcc <- cor(zcz);
pdf("SIGA.pdf", height=10,width=9)
heatmap.2(xcc, margins= c(9,9), col = bluered(64), trace=c("none"),
breaks=c(seq(-1,1,1/32)), symkey=TRUE, density.info="histogram",
cexRow=1)
I thank you all.
Paul
--
BEST
Paul Murima
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[R] Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + : must have one more break than colour
heatmap.2(m, margins= c(9,9), col = bluered(64), trace=c("none"),
breaks=c(seq(-60,0,60/20)), symkey=TRUE, density.info="histogram",
cexRow=1,)
Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + :
must have one more break than colour
Hie all.
I am working on scaling my data into a fited range of -60 0 and 60,
with increases of 20.
when i use heatmap,2 the error messgae i get is as follows
heatmap.2(m, margins= c(9,9), col = bluered(64), trace=c("none"),
breaks=c(seq(-60,0,60/20)), symkey=TRUE, density.info="histogram",
cexRow=1,)
Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + :
must have one more break than colour
Can any one help on how i can get around this problem.
Your help is most appreciated.
Rockie
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Re: [R] row labels in heatmap.2(package gplots)
Try Exporting to a Large pdfpdf("filename.pdf", width=20, height=20)
You can adjust the width and height accordingly
On Wed, Nov 26, 2008 at 4:30 AM, David Winsemius <[EMAIL PROTECTED]>wrote:
> I could not tell from the help file whether rotation of the x labels is
> supported in heatmap.2. I did read (perhaps in one of the linked to help
> files) that rotation was only allowed with "text" and I was left wondering
> if it might be possible to use text(x) and list(rot=90) as arguments to a
> scales call.
>
> At any rate, the results of this worked levelplot example from Sarkar's
> text is worth considering:
>
> data(Cars93, package="MASS")
> library(lattice)
> cor.Cars93 <- cor(Cars93[, !sapply(Cars93, is.factor)], use ="pair")
> levelplot(cor.Cars93, scales =list(x=list(rot=90)))
>
> --
> David Winsemius
>
>
> On Nov 25, 2008, at 2:19 PM, Jun Ding wrote:
>
> Dear R users,
>>
>> I have a question regarding how to make row labels readable in a heat map.
>>
>> I have successfully made a heat map using function "heatmap.2" in the
>> package "gplots". However, as there are many rows in the heat map, I have
>> difficulties labeling them (heatmap.2 provides a parameter "labRow" to label
>> the row names, but as I have too many rows, I can not make them readable).
>> Do you have any suggestions to improve the labeling?
>>
>> I am thinking about using multiple columns to label the row names instead
>> of one column(the default in heatmap.2). I have tried to use "mtext" to
>> write texts on the margin of the heat map, but it could not work either. Do
>> you think this can work? How can I know the coordinates of each row in a
>> heat map?
>>
>> Thank you very much!
>>
>> Jun
>>
>> __
>> R-help@r-project.org mailing list
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>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> __
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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and provide commented, minimal, self-contained, reproducible code.
[R] Null values In R.
Hi everyone.
I am having problems with NULL values. I understand in R one can
command the program to skip null values.
Can some one help me on the command line for that.
Do i enter is as part of the string in:
a<- read.table("filename.csv", header = T, row.names=1, sep=",");
My problem is largely when i attempt to use correlation for my data...
xcc <- cor(a);
The error i get is as follows
Error in cor(a) : missing observations in cov/cor
In addition: Warning message:
In cor(a) : NAs introduced by coercion
Regards
Paul Murima
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[R] Post Hoc methods for anova in R
Dear R community Does anyone know of some methods already programmed up open source in R for the post hoc methods in anova. I have some microarray data generated from different drug treatments 8 in particular, and a subset of 90 genes which i would like to analyseusing the above method. Thank you Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] concordance correlation coefficient using R
Hi. I have data which i would want to assess the degree of agreement between two assays, e.g., to evaluate reproducibility or for inter-rater reliability. I have used the Pearson product-moment correlation coefficient. It looks good ranginging between 0.90 to 0.998. Though this looks good. I am told the Concordance correlation coefficient will give a better picture of how reproducible the assay is. Does any one know how to run such a test using R? If so can you kindly provide the code, and bit of explanations to spruce it up? Thank you Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
