User: Wendy Qiao

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Wendy Qiao350
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Posts by Wendy Qiao

<prev • 34 results • page 1 of 4 • next >
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heatmap.2 with different colour ranges
... Hi all, I have a matrix with values between 0 and 1. I want to plot this matrix on a heat map so anything >0.05 is blue, anything <=0.05 and >0.01 is yellow, and anything else is grey. I am using the heatmap.2 function. I searched around but did not find an efficient way to set colour rang ...
written 5.8 years ago by Wendy Qiao350 • updated 5.8 years ago by Mercier Eloi60
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create GeneSetCollection from OBOCollection
... Hi all, I want to use GOStats for gene set enrichment with the GOslim collection. I find on the GO website that the generic GO slim collection is in the OBO format. I am trying to convert the OBOCollection to a gene set collection so I can use the GSEAGOHyperGparams function for GSEA. After hours ...
go convert gostats written 5.9 years ago by Wendy Qiao350
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convert GeneSetCollection to a list
... Hi all, I construct a GeneSetCollection objects from .gmt file using the following function TFT<-getGmt('c3.all.v3.0.entrez.gmt',geneIdType=EntrezIdentifier(),col lectionType=BroadCollection(category="c3")) I want to convert this GeneSetCollection object into a list with names identifying gene ...
convert written 6.1 years ago by Wendy Qiao350 • updated 6.1 years ago by Robert Castelo2.0k
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Comment: C: GSVA: using Entrez ID's as identifiers
... Hi Robert, Thank you for your reply. I happened to convert all the genes to hgu95a probe IDs as I found that this is the only platform that works with ExpressionSet. It would be great that we could make the entrez ID works. Following is my error that I got with your code. Thank you. Wendy > Bc ...
written 6.1 years ago by Wendy Qiao350
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GSVA: using Entrez ID's as identifiers
... Hi all, I am using the GSVA package for some analysis. I found that the package only takes the gene expression matrix annotated with affymetrix probe IDs, although the gene set collection is made of Entrez IDs. I imagine there a step in the package for converting the Affymetrix probe IDs to Entrez ...
probe gsva written 6.1 years ago by Wendy Qiao350 • updated 6.1 years ago by Robert Castelo2.0k
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making valid model matrix for using SNM package
... Hi all, I am trying to use the SNM package to normalize a dataset. The whole dataset is a combination of Illumina arrays and Affymetrix arrays. I use the batch effect to model the platform difference. Following is my code for constructing the bio.var and adj.var matrices. The SNM function gives an ...
snm written 6.1 years ago by Wendy Qiao350
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Comment: C: problem with using GSVA package
... Hi Robert, Thank you very much for your reply. I tried your comments. Everything worked fine until "make install". This comment gives the following errors. Any suggestion is appreciated. Thank you very much. Making install in gsl make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing ...
written 6.1 years ago by Wendy Qiao350
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problem with using GSVA package
... Hi all, I am trying to use the GSVA package, but I encounter the following problems. library(GSVA) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/GSVA/ libs/x86_64/GSVA.so': dlopen(/Library/Framewor ...
gsva written 6.1 years ago by Wendy Qiao350 • updated 6.1 years ago by Robert Castelo2.0k
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Comment: C: Convert gene expression matrix to ExpressionSet
... Thanks so much, Martin. It worked by updating R and Bioconductor packages! Wendy On 6 November 2011 23:33, Martin Morgan wrote: > On 11/06/2011 08:23 PM, Wendy Qiao wrote: > >> Thanks a lot, Martin. >> >> It is a good idea. The example in section 4.1 seems exactly what I ...
written 6.1 years ago by Wendy Qiao350
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Comment: C: Convert gene expression matrix to ExpressionSet
... Thanks a lot, Martin. It is a good idea. The example in section 4.1 seems exactly what I want, but it gives the following error. I wonder if you have any insight about this error. have checked Biobase manual. "ExpressionSet" is a valid function. I was wondering if you have any insight. Thank you ve ...
written 6.1 years ago by Wendy Qiao350

Latest awards to Wendy Qiao

Popular Question 5.8 years ago, created a question with more than 1,000 views. For package for collapsing probe id to entrezid or gene symbols
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Convert gene expression matrix to ExpressionSet

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