User: HKS

gravatar for HKS
HKS20
Reputation:
20
Status:
New User
Location:
Sweden
Last seen:
1 week, 3 days ago
Joined:
9 months ago
Email:
d********@gmail.com

Posts by HKS

<prev • 12 results • page 1 of 2 • next >
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how to get ER, PR and HER2 data from TCGA BRCA
... Hi I have dowloaded the BRCA data from TCGA using TCGABiolinks I have done this: BRCARnaseqSE <- GDCprepare(query.a, directory = "BRCA_all") sample.info <- SummarizedExperiment::colData(BRCARnaseqSE) Now I want to get data on ER, PR and HER2 - posotive, negative samples, but I ...
tcga brca pr her2 er written 10 days ago by HKS20 • updated 10 days ago by genomax85k
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retrieve TPM matrix from raw counts matrix or DESeq2 object dds
... Hi Is it possible to retrieve TPM from raw counts or DESeq2 object dds? I have downloaded the data from TCGA using ""TCGAbiolinks" package in R, although I have download the whole data set, I am making it simpler here, to download for a few samples, so that it will be easier for you to see this da ...
deseq2 tpm raw counts tcga brca written 5 weeks ago by HKS20 • updated 5 weeks ago by igor11k
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Comment: C: error in TXIMPORT command for RSEM
... And even if i do this: dds <- estimateSizeFactors(dds) counts(dds, normalized=TRUE) Will these normalized counts be equivalent to TPM? I think not, This is just dividing each column of counts(dds) by sizeFactors(dds) but it will not normalize for gene length, so I want TPM matrix from raw ...
written 5 weeks ago by HKS20
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Comment: C: error in TXIMPORT command for RSEM
... Now, I am able to get a dds object from DESeq2 package for this data using: dds <- DESeqDataSetFromMatrix(countData = BRCA_mat, colData = sampleData, design = ~ condition) I used "raw_counts" to generate "BRCA_mat" No ...
written 5 weeks ago by HKS20 • updated 5 weeks ago by Kevin Blighe61k
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Comment: C: error in TXIMPORT command for RSEM
... yes, i am sorry and thank you for being patient with me! this data is also new for me, so I followed these steps to download the data from TCGA using ""TCGAbiolinks" package in R, although I have download the whole data set, I am making it simpler here, to download for a few samples, so that it will ...
written 5 weeks ago by HKS20 • updated 5 weeks ago by Kevin Blighe61k
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Comment: C: error in TXIMPORT command for RSEM
... Hi, thanks, it makes sense, but I do not want to detect differentially expressed genes - I want to convert a matrix with counts (either raw or normalized) to TPM matrix, So count matrix that contains all samples in columns and all genes in rows can be converted into TPM matrix? ...
written 5 weeks ago by HKS20
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Comment: C: error in TXIMPORT command for RSEM
... yes, I agree, but I got to process this data I got from TCGA - BRCA (HTseq counts) project, to make a matrix of TPM. there are genes in the tmp obj starting from row 30 : > tmp[30:40,] # A tibble: 11 x 4 gene_id raw_count scaled_estimate transcript_id ...
written 6 weeks ago by HKS20 • updated 6 weeks ago by Kevin Blighe61k
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error in TXIMPORT command for RSEM
... Hi, I have downloaded the HT seq counts data (gene expression data) from TCGA for BRCA. I have files in *.rsem.genes.results format when I run command: txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE) It is giving me this error: reading in files with read_tsv ...
tximport rsem written 6 weeks ago by HKS20 • updated 6 weeks ago by Kevin Blighe61k
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Comment: C: error in tximport command
... Yes, you were right, thank you! ...
written 7 weeks ago by HKS20
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error in tximport command
... when I am typing command : `txi <- tximport(samples, type = "stringtie", tx2gene = tx2gene)` I am getting this error: Error in match.arg(type, c("none", "kallisto", "salmon", "sailfish", "rsem")) : 'arg' should be one of “none”, “kallisto”, “salmon”, “sailfish”, “rsem” I am using t_ ...
tximport written 7 weeks ago by HKS20 • updated 7 weeks ago by ATpoint36k

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