Displaying 9 results from an estimated 9 matches for "coexpressionnetwork".
2011 Jul 30
1
read.table only reads part of file
Hi all,
I encountered a problem when trying to read in an Illumina chip
annotation file. The offending file is large, so I zipped it up and
posted it at
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/tmp/ProbeInfo_Expression.txt.bz2
Executing this:
annot = read.table(bzfile("ProbeInfo_Expression.txt.bz2"),
comment.char="", sep = "\t", fill = TRUE, header = TRUE);
leads to
> dim(annot)
[1] 25952 28
i.e. 25952 rows were read, but the file...
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 =
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 <anku...
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
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
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