Error in proxy[i, ..., drop = FALSE] : incorrect number of dimensions

[swvanderlaan]

Hi,

First of all: thank you for this awesome package.

I am trying to combine to assays in one MultiAssayExperiment. When I use the try function it seems to be alright. See below. But when I try to actually combine them, it doesn't (see below). I don't get why not. What I am I missing/overlooking?

Thanks!

Sander

My try code:

cat("*Prepping and checking out the potential for a MultiAssayExperiment dataset ...\n")
objlist
dfmap
dim(AEDB_all)
try(prepMultiAssay(ExperimentList = objlist, colData = AEDB_all, sampleMap = dfmap)$experiments,
    outFile = stdout())

The try output:

*Prepping and checking out the potential for a MultiAssayExperiment dataset ...
$`AEMS450K1 blood (B-values)`
class: SummarizedExperiment 
dim: 276373 93 
metadata(4): creationDate author BBMRIomicsVersion note
assays(1): ''
rownames(276373): cg01707559 cg03244189 ... ch.22.46830341F ch.22.1008279F
rowData names(27): addressA addressB ... Regulatory_Feature_Group DHS
colnames(93): 8918692001_R01C02 8918692001_R05C01 ... 9221198164_R04C02 9221198164_R05C02
colData names(27): STUDY_NUMBER AEMS450K ... Basename ID

$`AEMS450K1 blood (M-values)`
class: SummarizedExperiment 
dim: 276373 93 
metadata(4): creationDate author BBMRIomicsVersion note
assays(1): ''
rownames(276373): cg01707559 cg03244189 ... ch.22.46830341F ch.22.1008279F
rowData names(27): addressA addressB ... Regulatory_Feature_Group DHS
colnames(93): 8918692001_R01C02 8918692001_R05C01 ... 9221198164_R04C02 9221198164_R05C02
colData names(27): STUDY_NUMBER AEMS450K ... Basename ID

DataFrame with 186 rows and 3 columns
                         assay   primary           colname
                      <factor> <numeric>       <character>
1   AEMS450K1 blood (B-values)       622 8918692001_R01C02
2   AEMS450K1 blood (B-values)      1409 8918692001_R05C01
3   AEMS450K1 blood (B-values)      1203 8918692002_R03C02
4   AEMS450K1 blood (B-values)       172 8918692002_R04C01
5   AEMS450K1 blood (B-values)        13 8918692004_R06C02
...                        ...       ...               ...
182 AEMS450K1 blood (M-values)      1324 9221197166_R04C02
183 AEMS450K1 blood (M-values)      1334 9221197166_R05C02
184 AEMS450K1 blood (M-values)       987 9221198164_R01C01
185 AEMS450K1 blood (M-values)      1230 9221198164_R04C02
186 AEMS450K1 blood (M-values)      1550 9221198164_R05C02
[1] 3727 1037
ExperimentList class object of length 2: 
 [1] AEMS450K1 blood (B-values): SummarizedExperiment with 276373 rows and 93 columns 
 [2] AEMS450K1 blood (M-values): SummarizedExperiment with 276373 rows and 93 columns 

My MultiAssayExperiment code:

AEMS450K.MultiAssay <- MultiAssayExperiment(experiments = objlist,
                                      colData = AEDB_all,
                                      sampleMap = dfmap)

The error message:

Error in proxy[i, ..., drop = FALSE] : incorrect number of dimensions

[LiNk-NY]

Hi Sander, @swvanderlaan It is difficult to reproduce your error without an small reproducible example.

You can use prepMultiAssay in the following way:

complist <- prepMultiAssay(ExperimentList, colData, sampleMap)

MultiAssayExperiment(
    experiments = complist[["experiments"]],
    colData = complist[["colData"]],
    sampleMap = complist[["sampleMap"]]
)

I hope this helps. Best, Marcel

[swvanderlaan]

Yes, sorry about not having the data. This https://github.com/waldronlab/MultiAssayExperiment/issues/277#issuecomment-634213625 option doesn't work. I get the same error.

Here is the traceback:

15. vec_index(x, i, ...) 
14. `[.vctrs_vctr`(structure(c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 3, NA, NA, 3, NA, 5, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 3, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... 
13. .Primitive("[")(structure(c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 3, NA, NA, 3, NA, 5, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 3, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... 
12. do.call(`[`, args) 
11. do.call(`[`, args) 
10. FUN(X[[i]], ...) 
9. FUN(X[[i]], ...) 
8. lapply(as.list(x), extractROWS, i) 
7. lapply(as.list(x), extractROWS, i) 
6. extractROWS(x, i) 5. extractROWS(x, i) 
4. colData[keep_colData, , drop = FALSE] 
3. colData[keep_colData, , drop = FALSE] 
2. .harmonize(experiments, colData, sampleMap) 
1. MultiAssayExperiment(experiments = objlist, colData = AEDB_all, sampleMap = dfmap)

I don't see what I am doing wrong:

• primary column in the sampleMap matches the colname column of the assay data (format: 8918692001_R01C02).
• primary column in the colData matches the primary column in the sampleMap.

This is the correct mapping, right?

And I have colData rows summing up to 186, which equals 2 assays of each 93 samples...

So what am I missing?

[LiNk-NY]

Hi Sander, @swvanderlaan

Unfortunately, I am unable to reproduce the issue with the examples that you provided. If you'd like further assistance, please provide a minimally reproducible example. https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

Best, Marcel

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