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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 Paired analysis in TCGAanalyze_DEA #440

Open 17ray opened 3 years ago

17ray commented 3 years ago

Hi, I want to perform pairwise differential analysis for BRCA tumor subtype Luminal A and normal sample. I have used the following code to download and process the data from TCGA using TCGAbiolinks package in R. But, when I am using paired = TRUE for TCGAanalyze_DEA, it is throwing me the following error:

Batch correction skipped since no factors provided ----------------------- DEA ------------------------------- there are Cond1 type Normal in 61 samples there are Cond2 type Tumor in 61 samples there are 8688 features as miRNA or genes I Need about 0 seconds for this DEA. [Processing 30k elements /s] Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent I have checked my matrices. The row and column sizes are same for both my matrices. I am not sure what is the issue. I used the following command: DEG_paired <- TCGAanalyze_DEA(mat1 = matched_NT_filt, mat2 = Matched_LumA, Cond1type = "Normal", Cond2type = "Tumor", fdr.cut = 0.05, logFC.cut = 1, method = "exactTest", pipeline = "edgeR", paired = TRUE)

Please help me.

Thanks, Kamalika

labrazil commented 3 years ago

You need to run an unpaired test.

Houtan

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On Tue, Dec 22, 2020, 03:40 17ray notifications@github.com wrote:

Hi, I want to perform pairwise differential analysis for BRCA tumor subtype Luminal A and normal sample. I have used the following code to download and process the data from TCGA using TCGAbiolinks package in R. But, when I am using paired = TRUE for TCGAanalyze_DEA, it is throwing me the following error:

Batch correction skipped since no factors provided ----------------------- DEA ------------------------------- there are Cond1 type Normal in 61 samples there are Cond2 type Tumor in 61 samples there are 8688 features as miRNA or genes I Need about 0 seconds for this DEA. [Processing 30k elements /s] Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent I have checked my matrices. The row and column sizes are same for both my matrices. I am not sure what is the issue. I used the following command: DEG_paired <- TCGAanalyze_DEA(mat1 = matched_NT_filt, mat2 = Matched_LumA, Cond1type = "Normal", Cond2type = "Tumor", fdr.cut = 0.05, logFC.cut = 1, method = "exactTest", pipeline = "edgeR", paired = TRUE)

Please help me.

Thanks, Kamalika

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17ray commented 3 years ago

Thank you for your reply. I would like to run paired differential analysis. I have tumor and normal samples of the same patients.