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kvittingseerup / IsoformSwitchAnalyzeR

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
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the output of importRdata is different? #248

Closed huawen-poppy closed 5 months ago

huawen-poppy commented 5 months ago

Hi! Thank you for your very nice tool!!

I am using below code to create switchAnalyzeRlist,

aSwitchList <- importRdata(
  isoformCountMatrix   = count,
  isoformRepExpression = tpm_data,
  designMatrix         = myDesign,
  isoformExonAnnoation = "./input_data/OUT.transcript_models.gtf",
  isoformNtFasta       = "./input_data/OUT.transcript_models.fa",
  )

at the first time the output looks like below:

Step 1 of 10: Checking data... Please note that some condition names were changed due to names not suited for modeling in R. Step 2 of 10: Obtaining annotation... importing GTF (this may take a while)... Step 3 of 10: Fixing StringTie gene annoation problems... There were no need to rescue any annotation Step 4 of 10: Calculating expression estimates from count data... Skipped as user supplied expression via the "isoformRepExpression" argument... Step 5 of 10: Testing for unwanted effects... No unwanted effects added Step 6 of 10: Batch correcting expression estimates... Step 7 of 10: Extracting data from each condition... |=============================================================================================================================================| 100% Step 8 of 10: Making comparisons... |=============================================================================================================================================| 100% Step 9 of 10: Making switchAnalyzeRlist object... Step 10 of 10: Guestimating differential usage... The GUESSTIMATED number of genes with differential isoform usage are: comparison estimated_genes_with_dtu 1 apo vs holo 108 - 181 Done

but when I run the same exact code, the output is different. is this normal? Step 1 of 10: Checking data... Please note that some condition names were changed due to names not suited for modeling in R. Step 2 of 10: Obtaining annotation... importing GTF (this may take a while)... Step 3 of 10: Fixing StringTie gene annoation problems... There were no need to rescue any annotation Step 4 of 10: Calculating expression estimates from count data... Skipped as user supplied expression via the "isoformRepExpression" argument... Step 5 of 10: Testing for unwanted effects... No unwanted effects added Step 6 of 10: Batch correcting expression estimates... Step 7 of 10: Extracting data from each condition... |=============================================================================================================================================| 100% Step 8 of 10: Making comparisons... |=============================================================================================================================================| 100% Step 9 of 10: Making switchAnalyzeRlist object... Step 10 of 10: Guestimating differential usage... The GUESSTIMATED number of genes with differential isoform usage are: comparison estimated_genes_with_dtu 1 apo vs holo 76 - 128 Done

chunxubioinfor commented 5 months ago

Hi @huawen-poppy, the guesstimated provided is just a guess informed by an estimate. This is provided for getting a quick idea of what to expect. The final number could be obtained after running isoformSwitchTestDEXSeq(), isoformSwitchTestSatuRn (), or other tools you like. I hope this is helpful to you. Please feel free to open a new issue if you need further help. ☺️