User: hamda.binte.ajmal

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Posts by hamda.binte.ajmal

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Comment: C: TCGAvisualize_EAbarplot Function Issue
... Hi, I am facing the same problem. Did you fix it? If yes, can you please share how? ...
written 19 months ago by hamda.binte.ajmal0
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LuminalA Breast cancer subtype samples from GEO GSE62944
... Hi All, is there a way to pull out samples of Luminal A subtype of breast cancer from TCGA data or GEO GSE62944? I did      library(AnnotationHub)     eh = AnnotationHub()     query(eh , "GSE62944")     tcga_data <- eh[["AH28855"]]     brca_data_lumA <- brca_data[, which(phenoData(brca_dat ...
cancer tcga gse62944 breastcancer luminala written 19 months ago by hamda.binte.ajmal0 • updated 19 months ago by phil.chapman120
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Comment: C: Normal Patient Samples from GSE62944
... Thank you for your reply Sonali. I was actually confused because I read on this post https://support.bioconductor.org/p/65890/#68096 That the normal samples have been added, so I wondered if there is any way to get them. Your replies are great help to me. Thanks alot   ...
written 19 months ago by hamda.binte.ajmal0
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Comment: C: failed to load 'AnnotationHub' resource
... Thank you so much. Works now ...
written 19 months ago by hamda.binte.ajmal0
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Normal Patient Samples from GSE62944
... Hello, I am trying to do Differential Expression Analysis of Genes of Normal vs. Breast cancer patients. For that ourpose, I chose GEO data GSE62944 as it contains  9264 Tumour Samples and 741 normal samples.  Question 1:  I load the expression set using code     library(AnnotationHub)     ah = ...
differentialexpression annotationhub gse62944 written 19 months ago by hamda.binte.ajmal0 • updated 19 months ago by Sonali Arora360
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Comment: C: Can I feed TCGA normalized count data to EdgeR for differential gene expression
... Thanks Stephen. This seems like a very promising resource. Do you have any help material as to how to load data into R as expressionSet , combine cancer and normal patients in one table and do the anaysis of cancer vs. non cancer data? ...
written 19 months ago by hamda.binte.ajmal0
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Comment: C: failed to load 'AnnotationHub' resource
... Still a problem for me.  hub = AnnotationHub() snapshotDate(): 2016-03-09 > gse = query(hub, "GSE62944")[[1]] Error: failed to load 'AnnotationHub' resource   name: AH28855   title: RNA-Sequencing and clinical data for 7706 tumor samples from The Cancer Genome Atlas   reason: 1 resources faile ...
written 19 months ago by hamda.binte.ajmal0
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Comment: C: Differential gene expression analysis for GSE62944
... sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_Ireland.1252  LC_CTYPE=English_Ireland.1252    LC_MONETARY=English_Ireland.1252 LC_NUMERIC=C                     [5] LC_TIME=E ...
written 19 months ago by hamda.binte.ajmal0
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Differential gene expression analysis for GSE62944
... Dear All, I am trying to do differtial gene expression analysis of Breast Cancer vs. normal patients using data set GSE62944.  biocLite("AnnotationHub") library(AnnotationHub) hub = AnnotationHub() Gives me error  downloading from ‘https://annotationhub.bioconductor.org/fetch/34295’ retrieving 1 ...
cancer limma R bioconductor tcga written 19 months ago by hamda.binte.ajmal0 • updated 19 months ago by Valerie Obenchain ♦♦ 6.4k

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