Workflow type=Star_counts, I want to download FPKM or TPM values, but star_counts for which?
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yuanyuan • 0
@980ae1b3
Last seen 22 months ago
United States

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Code should be placed in three backticks as shown below


query.exp.hg38 <- GDCquery(project ="TCGA-BRCA",
                           data.category = "Transcriptome Profiling",
                           data.type = "Gene Expression Quantification",
                           workflow.type = "STAR - Counts",
                           legacy = FALSE)#legacy=FALSE means we are download the data against hg38, otherwise it will be hg19
GDCdownload(query.exp.hg38, method = "api")
# Step 3: prepare the downloaded data (by default reading data from local folder C:/Users/dhe2/Documents/GDCdata/): 
maf <- GDCprepare(query.exp.hg38)
GDCquery • 2.6k views
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ATpoint ★ 4.0k
@atpoint-13662
Last seen 3 days ago
Germany

STAR - Counts is the raw counts, which is the best to start from for any analysis. If you want TPM and there is the gene length in that object use DESeq2: Is it possible to convert read counts to expression values via TPM and return these values? or alternatively use any of the common normalization methods from packages such as DESeq2 or edgeR/limma, check their manuals. By the way, it is appreciated if a post is not just code but at least some words to describe the problem outside of the title.

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Thanks for your response. But when I download the data as the above codes showed using workflow type=star counts, the results are not integer, please see below. If you said star-counts is the raw counts, the results should be integer, right? star_count[358,1:10] ENSG00000000003.15 ENSG00000000005.6 ENSG00000000419.13 ENSG00000000457.14 ENSG00000000460.17 ENSG00000000938.13 TCGA-E2-A15G-01A-11R-A12D-07 36.6937202639607 0.290333757414175 33.9243828855486 50.8754076453454 13.712686696331 6.90101008007539 ENSG00000000971.16 ENSG00000001036.14 ENSG00000001084.13 ENSG00000001167.14 TCGA-E2-A15G-01A-11R-A12D-07 18.5143603766424 27.4253733926621 77.2734462040804 68.5411001157002

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