in the file using 'read.table(data, head=T, fill=T), then the
data.frame in R will be:
abcd
1234
186NA
120NA
110NA
Could anyone tell me how to handle this?
Thank you very much,
Karena
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What R packages do you guys use for 'pathway analysis'? By 'pathway
analysis', I mean to check the enrichment of certain genes in KEGG | GO
pathways.
Thank you,
Karena
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Sent
Hi Dear all,
I am making some Venn Diagram plots in R.
http://r.789695.n4.nabble.com/file/n3919144/venn.0.001.jpg
This is one plot that I generated. What I want to do is to get rid of the
black boarder line. Is there any way to do this?
Thank you very much,
Karena
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Hi Dear all,
I am making Venn Diagram plots in R. I attached an example:
http://r.789695.n4.nabble.com/file/n3919206/venn.jpeg
I want to get rid of the black boarder line, is there any way to do it?
Thank you very much,
Karena
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write my 'aov' function? I am not sure about the
'random effects' part
i.e.
fm - aov(expression.level~tissue.type+Error(Sample.ID)+Error(batch),
data=sample)
??
Thank you,
karena
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Thank you so much, Gabor.
It works well!
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) in a chi-square distribution
is less than 0.05, then we will say H2 is accepted.
However, my problem is, I don't know how to specify these parameterizations
in 'lme' function based H0, H1 and H2, respectively. Can anyone help me with
that?
Thank you very much,
Karena
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Ok. Thank you.
karena
On Thu, Sep 15, 2011 at 5:33 PM, Bert Gunter [via R]
ml-node+s789695n3816961...@n4.nabble.com wrote:
You should post this to the r-sig-mixed-models list, not here.
-- Bert
On Thu, Sep 15, 2011 at 1:42 PM, karena [hidden
email]http://user/SendEmail.jtp?type
the numeric id on each node (0-99).
Can anyone tell me how to solve this problem?
Thank you,
Karena
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Thank you guys for all the help. I appreciate!
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Hi,
I want to generate multiple sets of random numbers.
The requirement is that:
1) each set have 3 random numbers;
2) the sum of the three number is always 1.
how to do this?
thank you,
karena
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To Jason: Still thank you, your reply gives me some clue about how to do
this.
To Duncan: Thank you for rely. It helped.
Karena
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Can anyone help me with this?
thank you in advance.
Karena
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use a string function to get the these number?
thanks,
karena
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Thank all you guys for the great help~. I appreciate
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Thanks a lot for the great help~
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can I convert this SAS
code to R code?
library(nlme)
fm - lme(trait~time+money, random=list(???), data=example)
How should I fill up the list()?
thank you very much,
Karena
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?
thank you very much,
karena
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Hi,
I am new to R.
My question is: how to get the 'hazard ratio' using the 'coxph' function in
'survival' package?
thanks,
karena
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is: how to get the value of 'per_se' for each gene?
thanks again.
Karena
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Thanks a lot for the great help, Timothy!
K
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the covariate adjustment to remove the effects of these two
covariates?
Should I do a 'step-wise' regression or something?
Which function in R should I use?
I am new to this field, and really appreciate your help!
thank you very much,
karena
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anyone help me on this?
thank you very much!
karena
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I am using 'igraph' package to make some graphs of 'gene-gene interaction'.
I can get a data.frame which has three columns.
gene1 gene2 pvalue
AGT MLR1.2e-04
MLR 11BHSD1 1.71e-05
IFG211BHSD2 2.2e-07
. . .
.
One more question is:
when you plot the gene network, you only get a number on each node, then how
can you match the numbers to the genes?
thank you very much,
Karena
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Thank you very much, Gabor! That helps.
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you very much!
karena
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https://stat.ethz.ch
-log10(results_chr_p$p). My question is: how to make multiple lines in one
plot, especially when using the 'running' function in it??
thank you very much,
karena
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try:ch
--
for(i in 1:22) {
chrn - paste(chr,i,sep=)
chrn=MEDIPS.readAlignedSeqences(BSgenome=hg19, file=chrn,numrows= )
chrn=MEDIPS.genomeVector(data=chrn, bin_size=50,extend=250)
...
...
write.table(frameschrn.frame500.step250, file=frames.chrn.meth.txt,
sep=\T, quote=F,
Hi, thank you very much for the help.
one more quick question: is that, my predictor variable should be coded as
'factor' when using either 'lm' or 'glm'?
sincerely,
karena
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Thanks a lot!
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2 1 1 0
so for this data set, what I wanna do is to replace all the '2' with '1',
how can I do it in an efficient way?
thank you,
karena
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Hi, do you guys know what function in R handles the multiple regression on
categorical predictor data. i.e, 'lm' is used to handle continuous predictor
data.
thanks,
karena
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this: when getting this
error message 'Error in MEEM...', directly goto the next variable?
thank you,
karena
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these seem something that I am looking for, I will try them, thank you!!
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Great! Thank you
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efficient way to do it?
thanks you very much,
karena
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0
The difference is for 'snp3', we can see, in 1) the values for snp3 are all
'00', while in 2) the values are all '0'. How can I keep the original
values for snp3 as '00', meanwhile get the 'headers' or say the colnames as
'snp1snp2snp3'?
thank you very much,
karena
)
---
## and I got the following error message:
Error in svd(X): infinite or missing values in 'x'.
I know this may be due to some missing data issue, but I just don't know how
to solve this problem.
anyone can help?
thanks a lot,
karena
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thank you, but even after I tried 'complete.cases' function, I still get the
same error messages.
help.
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data, then I performed the polygenic function with the complete
data.
thanks,
karena
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hey, guys, all these methods work perfectly. thank you!!
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funcname(folder/hyper.csv) # last line
anyone can tell me why is the difference?
thank you,
karena
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would be:
var3
ok
db
90
78
iojfodjfo
how to do this?
thanks,
karena
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R
to corr.iris, even when the (i==1 j==2) is not satisfied.
what's the problem here?
thanks,
karena
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yeah, both work. Thank you, guys...
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that makes sense. thank you, guys!
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19
326 3 20
how to calculate the summary value for each factor?
thanks
karena
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Thank you guys very much, these help!!
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, and for abd89C/T90, I
only want C and T, how to get these?
thank you,
karena
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much!
karena
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https://stat.ethz.ch
thank you guys very much!
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yeah, that's also working well, thanks!
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the following:
one = scan(three,1,'-')
two = scan(three,-1,'-')
How can I do this in R?
thank you,
karena
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Thank both of you guys!!
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in 1:100) {
write.table(, file='...', )
}
thank you,
karena
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in 1: 10) {
matrix_$i - matrix(nrow=i, ncol=i)
}
rather thank creating these matrices one by one manually.
Anyone have any suggestions?
thanks,
karena
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Thank you all for the great help...
I appreciate!
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thank all of you for the help.
to Petr: thanks for the suggestion, I will read the R intro manual.
:-)
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hi, I have a question about merging two files.
For example, I have two files, the first file is like the following:
id trait1
110.2
211.1
39.7
610.2
78.9
10 9.7
11 10.2
The second file is like the following:
idtrait2
1 9.8
2 10.8
4 7.8
5 9.8
6
and n4=0 and n5=0 then delete
the row. how can I do that?
thank you,
karena
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R
thank you very much!
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hi, I have a question about importing data in R.
I want to import a file which has missing value in it, and the missing
values are denoted as ., I want to first read in the file, and then change
the . into the number zero 0.
how can I do that?
thank you,
karena
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Hi, tim,
thank you very much for the reply, but I am really a new user. How to change
all NAs to zero?
thanks again.
karena
jholtman wrote:
?read.table
na.strings='.'
Then change all NAs to zero df$col[is.na(df$col)] - 0
On Tue, Jan 12, 2010 at 12:46 PM, karena dr.jz
thank you guys. All the columns of my data are numeric.
I tried both methods, and they both work.
I appreciate your help.
-k
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