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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Error in assay (or assays) function #489

Closed HeenaBioinfo closed 2 years ago

HeenaBioinfo commented 2 years ago

Hi I have downloaded isoform level data : it is having error in assay function: I want to extract raw counts and scaled estimates separately:

brca_iso <- GDCprepare(query = query.iso, directory = 'BRCA_iso', summarizedExperiment = TRUE)

brca_iso_raw <- assay(brca_iso,"raw_count")

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"data.frame", "character"’

I have tried this too:

Matrix_iso <- brca_iso[,seq(1,ncol(brca_iso),3)]

brca_iso_raw <- assay(Matrix_iso,"raw_count")

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"data.frame", "character"’

Please reply...

Thanks

Heena

tiagochst commented 2 years ago

Hi,

Please could you send the complete code?

I am not sure which files query.iso is pointing to.

Best regards, Tiago Chedraoui Silva

On Wed, Feb 2, 2022 at 1:12 PM HeenaSaini @.***> wrote:

Hi I have downloaded isoform level data : it is having error in assay function: I want to extract raw counts and scaled estimates separately:

brca_iso <- GDCprepare(query = query.iso, directory = 'BRCA_iso', summarizedExperiment = TRUE)

brca_iso_raw <- assay(brca_iso,"raw_count")

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"data.frame", "character"’

I have tried this too:

Matrix_iso <- brca_iso[,seq(1,ncol(brca_iso),3)]

brca_iso_raw <- assay(Matrix_iso,"raw_count")

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"data.frame", "character"’

Please reply...

Thanks

Heena

— Reply to this email directly, view it on GitHub https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/489, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQ6OCDWFM6UX3XGXG273UZFX2JANCNFSM5NMYXA4A . You are receiving this because you are subscribed to this thread.Message ID: @.***>

HeenaBioinfo commented 2 years ago

query.iso <- GDCquery(project = "TCGA-BRCA", data.category = "Gene expression", data.type = "Isoform expression quantification", experimental.strategy = "RNA-Seq", platform = "Illumina HiSeq", file.type = "results", legacy = TRUE)

HeenaBioinfo commented 2 years ago

If assay function doesn't work on data frames, I have tried converted it into matix too, it is still not working..

brca_iso_raw <- assay(as.matrix(brca_iso),"raw_count") Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"matrix", "character"’

HeenaBioinfo commented 2 years ago

Hi Tiago,

Any updates on my query?

tiagochst commented 2 years ago

Hi,

The output for isoforms is a dataframe. You can select the raw counts columns as follows:

library(TCGAbiolinks) query.iso <- GDCquery( project = "TCGA-BRCA", data.category = "Gene expression", data.type = "Isoform expression quantification", experimental.strategy = "RNA-Seq", platform = "Illumina HiSeq", file.type = "results", legacy = TRUE, barcode = c("TCGA-HN-A2NL","TCGA-D8-A27H") )

GDCdownload(query.iso)

data <- GDCprepare(query.iso) data_raw <- data[,grep("raw_count",colnames(data))]

On Mon, Feb 7, 2022 at 7:08 AM HeenaSaini @.***> wrote:

Hi Tiago,

Any updates on my query?

— Reply to this email directly, view it on GitHub https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/489#issuecomment-1031396094, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQ6OF7DCQNONTZRUROOLUZ6Y3RANCNFSM5NMYXA4A . You are receiving this because you commented.Message ID: @.***>

HeenaBioinfo commented 2 years ago

Thank you Tiago,

it was an R function afterwards.. I thought there was some problem with the "assay" function..

Thanks for your time..