User: Lourdes Peña Castillo
Lourdes Peña Castillo • 140
- Reputation:
- 140
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- Trusted
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- Last seen:
- 7 years, 8 months ago
- Joined:
- 14 years, 4 months ago
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- l***********@gmail.com
Posts by Lourdes Peña Castillo
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... Hello,
I am using the re-annotation of Illumina probe sequences available in
the
IlluminaMousev2.db (great package!), and I have two questions (please
see
code below as well):
1) Is there any difference between Good and Good*** or Perfect and
Perfect**** probe quality?
2) I noticed there are two ...
written 7.7 years ago by
Lourdes Peña Castillo • 140
0
votes
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3.5k
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1
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... Hello Everyone,
I have encountered an unexpected behaviour in limma vennDiagram
function and
I am unsure whether that is the intended behaviour and if so, what the
interpretation is.
Here are the versions I am using:
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0 ...
written 8.7 years ago by
Lourdes Peña Castillo • 140
• updated
8.7 years ago by
James W. MacDonald ♦ 51k
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499
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... Dear all,
I want to use SPIA to analyze expression data for rice (oriza sativa -
osa). There is KEGG's pathway data for rice, but rice is not among
those
organism in the extData directory of the SPIA package. Does anyone
has
created their own pathway data to give it as input to the function
spia? ...
written 8.9 years ago by
Lourdes Peña Castillo • 140
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2
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454
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2
answers
Answer:
A: subsetting in limma
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written 13.7 years ago by
Lourdes Peña Castillo • 140
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written 13.9 years ago by
Lourdes Peña Castillo • 140
0
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3
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3.4k
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3
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... Hi Ann,
> Using the heatmap function, is there a way to suppress the column
> reordering and column dendrogram? I have five time points and I
want to
> keep them in order! I have tried the following commands, but still
get
> reordered columns:
>
> heatmap(x, Colv=FALSE.. ...
written 14.0 years ago by
Lourdes Peña Castillo • 140
0
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548
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... Hello Everyone,
I need to get the most specific common ancestor for several GO terms.
I get the ancestors for the GO-terms (using mget(goTerms,
GOBPANCESTOR) ) and intersect the lists without problem, but I haven't
found a way to determine which GO-term from the common ancestor list
is the most sp ...
written 14.0 years ago by
Lourdes Peña Castillo • 140
0
votes
1
answer
510
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1
answer
... Hello Everyone,
I am trying to use GO for statistical analysis and I have several
questions which I hope you could help me to answer.
1. How can I change configuration parameters from a goCluster object
without running again config(goCluster_object)? Alternatively, where
could I find documentatio ...
written 14.1 years ago by
Lourdes Peña Castillo • 140
• updated
14.1 years ago by
Gunnar Wrobel • 60
0
votes
1
answer
425
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1
answer
... Hello,
I am following step by step the benomyl example in the GOCluster user
manual and when trying to display the hierarchical clustering results,
I get the following error:
> display(benomylExecuted, selection = 2)
Error in text.default(tp + 0.1, textpoint, axis[c2, 3], 0, cex = ts) :
...
written 14.2 years ago by
Lourdes Peña Castillo • 140
• updated
14.2 years ago by
Seth Falcon • 7.4k
0
votes
1
answer
1.3k
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1
answer
... Hello,
I am using limma to select differentially expressed genes. I have 24
arrays and 40k genes. According to the limma users' guide, "If none of
the raw p-value are less than 1/G, where G is the number of genes,
then all of the adjusted p-values will be
equal to 1".
I get raw p-values which are ...
written 14.2 years ago by
Lourdes Peña Castillo • 140
• updated
14.2 years ago by
James W. MacDonald ♦ 51k
Latest awards to Lourdes Peña Castillo
Popular Question
7.7 years ago,
created a question with more than 1,000 views.
For adjusted p-values for large number of genes...
Popular Question
7.7 years ago,
created a question with more than 1,000 views.
For Limma vennDiagram function
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