User: Lourdes Peña Castillo

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Posts by Lourdes Peña Castillo

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IlluminaMousev2.db probe quality information questions?
... 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 ...
probe convert written 7.8 years ago by Lourdes Peña Castillo140
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Limma vennDiagram function
... 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 ...
limma written 8.8 years ago by Lourdes Peña Castillo140 • updated 8.8 years ago by James W. MacDonald52k
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How to create KEGG's pathway data for SPIA?
... 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? ...
spia written 9.0 years ago by Lourdes Peña Castillo140
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Answer: A: subsetting in limma
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written 13.9 years ago by Lourdes Peña Castillo140
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Answer: A: omit row dendrogram in heatmap
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written 14.0 years ago by Lourdes Peña Castillo140
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Answer: A: heatmap-suppress col reordering/dendrogram?
... 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 14.1 years ago by Lourdes Peña Castillo140
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Most specific common ancestor for GO terms
... 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 ...
go written 14.2 years ago by Lourdes Peña Castillo140
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Several questions goCluster and GOstats...
... 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 ...
annotation go visualization yeast gocluster written 14.3 years ago by Lourdes Peña Castillo140 • updated 14.3 years ago by Gunnar Wrobel60
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Display error - GoCluster user manual
... 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) : ...
clustering gocluster written 14.3 years ago by Lourdes Peña Castillo140 • updated 14.3 years ago by Seth Falcon7.4k
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adjusted p-values for large number of genes...
... 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 ...
limma written 14.3 years ago by Lourdes Peña Castillo140 • updated 14.3 years ago by James W. MacDonald52k

Latest awards to Lourdes Peña Castillo

Popular Question 7.8 years ago, created a question with more than 1,000 views. For adjusted p-values for large number of genes...
Popular Question 7.8 years ago, created a question with more than 1,000 views. For Limma vennDiagram function

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