Error in validObject

[mfcesur]

Dear Dr. Steinbaugh,

I would like to perform differential expression analysis via bcbioRNASeq package. Even if I installed this package according to the instructions in the code page (https://github.com/hbc/bcbioRNASeq), I got the following error for counts function:

"raw_count <- counts(bcb, normalized = FALSE) Error in validObject(object) : invalid class “bcbioRNASeq” object: Legacy metadata: 'template', 'rowRangesMetadata', 'utilsSessionInfo', 'devtoolsSessionInfo' If supported, 'updateObject' may help resolve these issues."

I would greatly appreciate if you could provide your comments or suggestions on the error. Note that I am using the last version of R.

Sincerely, Müberra

[mjsteinbaugh]

Hi @mfcesur , thanks for getting in touch. Likely what's going on here is that your bcb object was saved with a legacy version of bcbioRNASeq (i.e. the bioconda version bundled with bcbio-nextgen) and then loaded into an R session running a newer version of the package.

Try this first and see if it resolves your issue:

bcb <- updateObject(bcb)
raw_count <- counts(bcb, normalized = FALSE)

If not then I need to push a bug fix to the package to help resolve your issue. I'll also work on making this error message a bit more informative, about how to use updateObject in practice.

Best, Mike

[mjsteinbaugh]

Also for reference, here's how to dive into the structure of the bcbioRNASeq object a bit more, which can be helpful for debugging. Your object should look like this after calling updateObject:

library(bcbioRNASeq)
data(bcb)
names(metadata(bcb))
##  [1] "allSamples"          "bcbioCommandsLog"    "bcbioLog"
##  [4] "call"                "caller"              "countsFromAbundance"
##  [7] "dataVersions"        "date"                "ensemblRelease"
## [10] "fast"                "genomeBuild"         "gffFile"
## [13] "interestingGroups"   "lanes"               "level"
## [16] "organism"            "packageVersion"      "programVersions"
## [19] "projectDir"          "runDate"             "sampleDirs"
## [22] "sampleMetadataFile"  "sessionInfo"         "tx2gene"
## [25] "uploadDir"           "wd"                  "yaml"
slotNames(bcb)
## [1] "rowRanges"       "colData"         "assays"          "NAMES"
## [5] "elementMetadata" "metadata"
assayNames(bcb)
## [1] "counts"      "aligned"     "avgTxLength" "tpm"         "normalized"
## [6] "vst"         "fpkm"

[mfcesur]

Use of the updateObject function solved this issue. Thank you so much for your consideration.

Kind regards, Müberra