User: Javerjung Sandhu

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Posts by Javerjung Sandhu

<prev • 19 results • page 2 of 2 • next >
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GAGE Package: Problem with Affymetrix hg u133 plus 2 probeset IDs conversion to Gene names or vice versa
... Dear list, I have expression data with Affymetrix hg u133 plus 2 probeset IDs & gene set data with gene names. So both gene set and expression data are not using the same gene ID system which is a requirement to run the GAGE analysis. So the problem is that if i convert the Probeset IDs to gene ...
convert gage written 7.4 years ago by Javerjung Sandhu200
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GAGE Question
... Dear list, For GAGE package, I converted Affymetrix hg u133 plus 2 probeset IDs to gene names so that both "exprs" and "gsets" use same gene ID system. But when i got the results from Biomart, the data showed different probe IDs corresponding to same gene name. So if i have to replace the probe IDs ...
probe biomart gage written 7.4 years ago by Javerjung Sandhu200
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Answer: A: Error in GAGE analysis, help URGENTLY required
... ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] On Behalf Of Javerjung Sandhu [jsandhu@bcgsc.ca] Sent: Friday, February 24, 2012 4:03 PM To: bioconductor at r-project.org Cc: luo_weijun at yahoo.com Subject: [BioC] Error in GA ...
written 7.4 years ago by Javerjung Sandhu200
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Error in GAGE analysis, help URGENTLY required
... Dear list, For the GAGE analysis, i am getting an error shown below. Error in rank(cns) : unimplemented type 'NULL' in 'greater' In addition: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' I got the gene sets, expression data and reference and target files read ...
gage written 7.4 years ago by Javerjung Sandhu200
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Error in GAGE analysis
... chr5q23 do_not_care PTMAP2 FTMT PRR16 MGC32805 MRPS5P3 LOC402229 RPS17P2 LOC728460 GPX3 GDF9 LOX NRG2 EGR1 ARGFXP1 CDO1 UBE2B RAD50 NME5 DTWD2 TNFAIP8 SLC27A6 CSNK1G3 ADAMTS2 CSF2 LOC389322 LMNB1 FLJ33630 CTXN3 SNX2 ACTBP4 PRRC1 GRA ...
trio written 7.4 years ago by Javerjung Sandhu200
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Answer: A: FW: URGENT Help required: Getting this error with GAGE analysis, input files att
... Hi Martin, Thanks for the super quick reply. Now i am getting this error.Why i am getting this error. > #!/usr/bin/R > library(gage) > Micro_array_data <- data.matrix(readExpData(file = "Micro_array_dataset.txt")) > Gene_set <- readList("c1_all_v3_0_symbols.gmt") > Reference_con ...
written 7.5 years ago by Javerjung Sandhu200
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Answer: A: How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE an
... Hello Valerie, Thanks for your help. I am sending you the data files(Micro_array_dataset.txt** & Gene_Set.txt) which i want to use for the analysis. I need to know in which format the files should be saved (like http:// www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_format s thi ...
written 7.5 years ago by Javerjung Sandhu200
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Answer: A: How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE an
... Dear List, I will highly appreciate your help on this. For the GAGE analysis package shown by the link given below: http://www.bioconductor.org/packages/release/bioc/html/gage.html Could you please tell me how to prepare the Custom INPUT files required for this analysis OR Send me the SAMPLE DATA fi ...
written 7.5 years ago by Javerjung Sandhu200
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How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files
... Hi there, For the GAGE analysis package shown by the link given below: http://www.bioconductor.org/packages/release/bioc/html/gage.html Could you please tell me how to prepare the Custom INPUT files required for this analysis OR Send me the SAMPLE DATA files in TXT format so that i know in which for ...
gage written 7.5 years ago by Javerjung Sandhu200

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Popular Question 7.2 years ago, created a question with more than 1,000 views. For Few errors with edgeR

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