Displaying 20 results from an estimated 700 matches similar to: "read.table only reads part of file"
2017 Jul 09
0
Error in WGCNA package
First, please read WGCNA FAQ at
https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html
regarding using RNA-seq and other count data.
Second, if you insist on using WGCNA on raw count data (which I don't
recommend), use something like
storage.mode(datExpr) = "double"
and try again.
Peter
On Sun, Jul 9, 2017 at 2:29 AM, Ankush Sharma <ankush.sak at
2017 Jul 09
1
Error in WGCNA package
Dear all ,
I would like to reconstruct coexpression networks from proteomic count data
having integer values. Some internal function doesn't like to work well
with integers. How can this error be rectified?
> adjacency = adjacency(datExpr, power = softPower, type = "signed");
Error in cor(datExpr, use = "p") :
REAL() can only be applied to a 'numeric', not a
2011 Sep 12
1
hclust and cutree: identifying branches as classes
Good afternoon,
After cuting a hierarchical tree using cutree(), how to check correspondances between classes and branches?
This is what we do:
srndpchc <- hclust(dist(srndpc$x[1:1000,1:3]),method="ward") #creation of hierarchical tree
plclust(srndpchc,hmin=20000) #visualisation
srndpchc20000 = cutree(srndpchc,h=20000) #returns 4 classes
table(srndpchc20000 )
srndclass20000 =
2010 Sep 29
1
cor() alternative for huge data set
Hi,
I am have a data set of around 43000 probes(rows), and have to calculate correlation matrix. When I run cor function in R, its throwing an error message of RAM shortage which was obvious for such huge number of rows. I am not getting a logical way to cut off this huge number of entities, is there an alternative to pearson correlation or with other dist() methods calculation(euclidean) that
2012 Mar 15
1
Get Details About Clusters
Hi everybody!
Anybody knows how can I get detalied information about clusters after using hclust?
The issue is that if I have some items in different clusters, I would like to get the cluster where each item is placed.
Taking into account that my data set is too large, it is not useful to have the dendogram or a graphic, and really I need something like a simple table with item label and cluster
2010 Jun 23
5
Plotrix Trick
Dear All,
I am using the plotrix library to plot some matrices.
I have a problem: some of my data are outliers, hence using a linear
color scale does not work very well (you would see too many cells having
a similar, indistinguishable color). See the code snipped at the end of
the email.
Plotting the logarithm of the data gets the job done, but my problem is
that I would like to write in every
2012 May 24
4
Manually modifying an hclust dendrogram to remove singletons
Dear R-Help,
I have a clustering problem with hclust that I hope someone can help
me with. Consider the classic hclust example:
hc <- hclust(dist(USArrests), "ave")
plot(hc)
I would like to cut the tree up in such a way so as to avoid small
clusters, so that we get a minimum number of items in each cluster,
and therefore avoid singletons. e.g. in this example, you can see
2008 Jan 21
2
reordering huge data file
Dear R-experts,
My problem is how to handle a 10GB data file containing genotype data. The file is in a particular format (Illumina final report) and needs to be altered and merged with phenotype data for further analysis.
PERL seems to be an frequently used solution for this type of work, however I am inclined to think it should be doable with R.
How do I open a text-file, line by line,
2011 Apr 09
3
In need of help with correlations
I am in need of someone's help in correlating gene expression. I'm somewhat
new to R, and can't seem to find anyone local to help me with what I think
is a simple problem.
I need to obtain pearson and spearman correlation coefficients, and
corresponding p-values for all of the genes in my dataset that correlate to
one specific gene of interest. I'm working with mouse Affymetrix
2004 Sep 24
3
Error with repeat lines() in function
I have a function that does some plotting. I then add lines to the
plot. If executed one line at a time, there is not a problem. If I
execute the function, though, I get:
Error in ans[[1]] : subscript out of bounds
This always occurs after the second lines command, and doesn't happen
with all of my data points (some do not have errors). Any ideas?
Thanks,
Sean
2009 Apr 21
2
DNAcopy package in R
Hi All:
Has anyone analyzed Illumina 550K data using DNAcopy package? I have around
2300 samples. According to
Venkatraman and Olshen 2007 paper, it needs about 25 min to run a single
sample for Affymetrix 100K. I am afraid it will take too long to analyzed my
data. Anybody has an idea? Thanks!
Best,
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2010 Dec 09
1
Complete newbie - create microarray image from data file?
Hey
So sorry to be a total newbie, but i'm just finding my feet with R.
I heard on the grapevine i could recreate a scanned microarray image, or at
least get a good graphic of it from a just a data file.
I have .txt files for illumina beadarrays but no images cos the service we
used didn't send them. The 'beadarray' package seems to require TIFFs to get
the graphic output.
Does
2012 Sep 19
2
write.table: strange output has been produced
Good afternoon all -
While making a steady progress in learning R after Matlab I encountered
a problem which seems to require some extra help to move over.
Basically I want to merge a data from biological statistical dataset
with annotation data extracted from another dataset using an 'id'
crossreference and write it to report file. The first part goes
absolutely fine, I have merged both
2012 Jun 12
2
Error in sort(abs(diff(genomdat)))[1:n.keep] : only 0's may be mixed with negative subscripts
Hello everyone,
I`m trying to normalize and analize an illumina SNP array.
But when i`m trying to segmentate i`m getting an error:
Error in sort(abs(diff(genomdat)))[1:n.keep] :
only 0's may be mixed with negative subscripts.
I`ve tried everything to fix this but the error still occours.
Can anybody give me a tip?
Thanks in advance!
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2010 Jan 08
10
[Bug 25952] New: GeForce 9800 GTX - nouveau_init takes ~ 1 minute to complete
http://bugs.freedesktop.org/show_bug.cgi?id=25952
Summary: GeForce 9800 GTX - nouveau_init takes ~ 1 minute to
complete
Product: xorg
Version: unspecified
Platform: Other
OS/Version: All
Status: NEW
Severity: major
Priority: high
Component: Driver/nouveau
AssignedTo: nouveau at
2009 Mar 13
2
No reply to our critical packet
Hi,
I?ve installed Asterisk for use as a SIP server. I can call people, but one
strange thing happens: if I call someone with a SIP account outside my server
(for example, sip:enum-echo-test at sip.nemox.net) everything is fine, if I call
any Asterisk extension it also works, but the call gets disconnected in about
20 seconds. To be exact, audio is turned off but the SIP client still thinks
2007 Jun 21
2
segfault during cbind
The following code results in a seg fault.
> sessionInfo()
R version 2.6.0 Under development (unstable) (2007-06-21 r42013)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics
2009 Apr 20
1
generic genotype calling algorithm?
Hi,
I have Agilent and Illumina SNP data. That's the only thing I know about the
files - there seem to be no version specification in any of them.
Is there a generic genotype calling algorithm that I could try to use on
these datasets?
thanks,
N.
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Sent from the R help
2008 Oct 23
3
xy.coords in text
Hello,
I want to add text annotation about correlation on "pairs" plots. I
found that I could pass a function to the "panel" argument of pairs :
panel.annot <- function(x, y, ...) {
points(x, y, ...)
c <- cor.test(x, y)
legend("topleft", legend=substitute(rho == r, list(r=sprintf("%.2f",
c$estimate))), bty="n")
}
And then :
2008 Mar 20
2
Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"
Hello Everyone,
I am writing programs in R from 7 months and I am able to solve most of the
errors/issues except for this current post.
My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains
the Microarray Expression Values collected from the Illumina Microarray
experiment. These collected intensity values need to be normalized(Rank
Invariant Normalization) by using the R