Workflow type=Star_counts, I want to download FPKM or TPM values, but star_counts for which?
1
0
Entering edit mode
yuanyuan • 0
@980ae1b3
Last seen 2.5 years ago
United States

Enter the body of text here

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 • 3.3k views
ADD COMMENT
0
Entering edit mode
ATpoint ★ 4.6k
@atpoint-13662
Last seen 13 hours 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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 610 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6