Question: A question about DEXSeq of estimateDispersions
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gravatar for liushang
4 weeks ago by
liushang0
liushang0 wrote:

HI, I meet an error when I run a 119311* 749 dataframe:

       error: matrix multiplication: incompatible matrix dimensions: 1498x751 and 0x1
       Error in fitBeta(ySEXP = ySEXP, xSEXP = xSEXP, nfSEXP = nfSEXP, alpha_hatSEXP = alpha_hatSEXP,  :
       matrix multiplication: incompatible matrix dimensions: 1498x751 and 0x1
       Calls: estimateDispersions ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
       Execution halted

using the command:

      matall=cbind(mat_filter,mat_used) ## the 119311 * 749 datatframe
      sampleData <- data.frame(condition = c(rep('filter',length(colnames(mat_filter))),rep('used',length(colnames(mat_used)))))
      groupID <- as.character(rowann$V3)
      featureID <- as.character(rowann$V1)
      design <- formula( ~ sample + exon + condition:exon  )
      dim(matall)
      dim(sampleData)
      length(groupID)
      all <- DEXSeqDataSet( matall, sampleData, design,featureID, groupID)
      dxd <- all
      dxd = estimateSizeFactors( dxd )
      dxd = estimateDispersions( dxd )

I guess that the error results from the large dataframe, so I creat a 119311 * 10 dataframe from the 119311 * 749 datatframe, and then it works and didnot produce the error.

Any help is greatly appreciated.

dexseq • 53 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by liushang0
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