Persistent stageWiseAdjustment error

[manueltar]

Hi,

First of all thank you very much for the package and the support. I have encountered an error similar to the stageWiseAdjustment error #8 that was closed after fixing a bug with the allowNA option. I have reinstalled from github stageR and the error persists and I have filtered the NA's prior to the stageWiseAdjustment and the error persists.

My log prints:

..$ stageR :List of 29
.. ..$ Package : chr "stageR"
.. ..$ Type : chr "Package"
.. ..$ Title : chr "stageR: stage-wise analysis of high throughput gene expression\ndata in R"
.. ..$ Version : chr "1.7.01"

pScreen_0
Named num [1:15] 5.34e-61 7.03e-05 4.94e-04 2.57e-01 1.02e-06 ...

• attr(*, "names")= chr [1:15] "ENSG00000100299" "ENSG00000025708" "ENSG00000130489" "ENSG00000025770" ...

pConfirmation_0
num [1:48, 1] 1.40e-54 8.75e-33 1.00 1.00 1.00 ...

• attr(*, "names")= chr [1:48] "ENST00000216124" "ENST00000356098" "ENST00000453344" "ENST00000551731" ...

tx2gene_0
'data.frame': 48 obs. of 2 variables:
$ feature_id: chr "ENST00000216124" "ENST00000356098" "ENST00000453344" "ENST00000551731" ...
$ gene_id : chr "ENSG00000100299" "ENSG00000100299" "ENSG00000100299" "ENSG00000100299" ...

stageRObj <- stageRTx(pScreen=pScreen, pConfirmation=pConfirmation,
pScreenAdjusted=FALSE, tx2gene=tx2gene)

stageRObj_0
Formal class 'stageRTx' [package "stageR"] with 15 slots
  ..@ pScreen        : Named num [1:15] 5.34e-61 7.03e-05 4.94e-04 2.57e-01 1.02e-06 ...
  .. ..- attr(*, "names")= chr [1:15] "ENSG00000100299" "ENSG00000025708" "ENSG00000130489" "ENSG00000025770" ...
  ..@ pConfirmation  : num [1:48, 1] 1.40e-54 8.75e-33 1.00 1.00 1.00 ...
  .. ..- attr(*, "names")= chr [1:48] "ENST00000216124" "ENST00000356098" "ENST00000453344" "ENST00000551731" ...
  ..@ adjustedP      : num[0 , 0 ]
  ..@ method         : chr(0)
  ..@ alpha          : num(0)
  ..@ alphaAdjusted  : num(0)
  ..@ adjusted       : logi FALSE
  ..@ pScreenAdjusted: logi FALSE
  ..@ tx2gene        :'data.frame':     48 obs. of  2 variables:
  .. ..$ feature_id: chr [1:48] "ENST00000216124" "ENST00000356098" "ENST00000453344" "ENST00000551731" ...
  .. ..$ gene_id   : chr [1:48] "ENSG00000100299" "ENSG00000100299" "ENSG00000100299" "ENSG00000100299" ...

and in the next step it crashes:

stageRObj <- stageWiseAdjustment(stageRObj, method="dtu", alpha=0.05)

Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent
Calls: system.time ... stageWiseAdjustment -> .local -> .stageWiseTest -> rownames<-

I am happy to provide the files with the values. Best regards

[alejandrogzi]

Hi @manueltar,

Did you find a solution? I am having a similar problem with the same function. However, I am getting this error:

Error in [<-(tmp, idCon, 1, valué = unlist(txLevelAdjustments)) : subscript out of bounds.

I have been debugging most of "stageWiseAdjustment" method and each code chunk runs perfectly with my data (which is very similar to the DTU tutorial by Love, Soneson & Patro (2018)).

[koenvandenberge]

Hi both,

Apologies for the delay. Could you please provide a reproducible example (using either simulated or your real data) such that I am able to dig in further?

Thanks,
Koen