User: ying chen

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ying chen340
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Posts by ying chen

<prev • 34 results • page 1 of 4 • next >
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Comment: C: affy( ) error with mas5()
... Hi guys, Thanks a lot for the help and sorry for getting back to you so late :(. Now I got confused. Does it mean affy() cannot do a MAS5 of 3869 HG- U133_Plus_2 arrays with affy CDF because of the setting of R long vectors, or I did something wrong? I did a RMA with no problem. Thanks, Ying &g ...
written 5.6 years ago by ying chen340
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Comment: C: countOverlaps Warnings
... Hi Martin, Thanks a lot for the help! I believe it's due to some virus on my computer as I just found out that my computer's antivirus programs all got turned off and could not be turned back on. I am re-installing Windows now and will try to re-install R and googleVis later. Thanks, Ying > D ...
written 5.6 years ago by ying chen340
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Comment: C: countOverlaps Warnings
... Hi guys, I have this weird error when I tried to install googleVis package. I installed it in my other PC with no problem and both runs Win7 Enterprise 64x. I tired to install from biocLite("googleVis"), install.packages("googleVis"), install.packages() from downloaded source, and had the same erro ...
written 5.6 years ago by ying chen340
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Comment: C: Comparison of murine and human microarray data
... Hi Matt, I just wonder is it possible for you to update the hgu133plus2frmavecs packages to use the most recent customCDF v18? Thanks a lot, Ying > Date: Tue, 22 Apr 2014 10:40:33 -0400 > From: mccallm@gmail.com > To: sbrohee@ulb.ac.be > CC: basvgestel@hotmail.com; bioconductor@r-pro ...
written 5.6 years ago by ying chen340
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Answer: A: edgeR design matrix, one group vs average of other groups
... Hi guys, I tried to draw plots similar to cbioportal's oncoprint plot, but have no success yet. Here is an example of the oncoprint plot: http://www.cbioportal.org/public-portal/index.do?cancer_study_id=luad_ tcga&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=luad_tcga_mutations &genetic_pro ...
written 5.8 years ago by ying chen340
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Answer: A: Gviz: axes related parameters
... Hi guys, I encounter this kind question quite a few times now and never have a good answer. Say we have the expression data (microarray or RNAseq) of gene A for both tumor and normal samples. The task is to detect how many tumor samples have gene A over-expressed. I had tried to use mean+2*stdev of ...
written 5.8 years ago by ying chen340
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Answer: A: EdgeR norm.factors input
... Hi guys, I just got this weird error with CNTools package. Basically I tried to map TCGA SNP6 level3 segmentation data to gene level. I have TCGA SNP6 level3 segmentation data fpor more than 16000 samples. All processed well except for a block of 300 samples, which gave me the following error messag ...
written 5.8 years ago by ying chen340
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Comment: C: Plots with transparent background in ggbio.
... Hi guys, I tried to install affxparser in R3.0.1 in Cygwin x64, but got some errors. Makevars:4: recipe for target `fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o' failed make: *** [fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o] Error 1 ERROR: compilation failed for package ‘affxparse ...
written 6.2 years ago by ying chen340
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Comment: C: XML package - 500 internal server error
... Hi guys, I tried a sample with Variant Annotation's eadVcf. I ran the code successfully in Linux (OK I had some warnings regarding " unpackVcf field '..': NAs introduced by coercion"). But when I tried the same code in R3.0.0 in windows 7, I got the error message: > for(i in 1:length(vcflist1)){ ...
written 6.6 years ago by ying chen340
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Help needed! What wrong with VariantAnnotation and TCGA vcfs
... Hi guys, sorry to bother you again. I am new to VariantAnnotation package and keep having some weird errors when testing with TCGA vcfs. > start.loc <- 55086725 > end.loc <- 55275031 > test.gr <- GRanges("7", IRanges(start.loc, end.loc)) > file <- system.file("vcf", "NA0698 ...
variantannotation genomes written 6.7 years ago by ying chen340 • updated 6.7 years ago by Martin Morgan ♦♦ 24k

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