Error in MetaQC R package.
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@agaz-hussain-wani-7620
Last seen 3.5 years ago
India

I am trying to perform Meta-analysis to verify the quality of micro-array studies. I have a list of two studies with eight samples in each.

testdf
$agaz
                  1          1            1          1            2          2            2          2
ID          1.00000    2.00000    1.0000000    2.00000    1.0000000    2.00000    1.0000000    2.00000
SLC20A1  3242.90209 3242.90209  242.9020870 3242.90209  242.9020870 3242.90209  242.9020870 3242.90209
PRDX4     377.81481  377.81481   77.8148132  377.81481   77.8148132  377.81481   77.8148132  377.81481
MCM6      114.88743  114.88743   14.8874270  114.88743   14.8874270  114.88743   14.8874270  114.88743
HEXB     8739.03257 8739.03257  739.0325730 8739.03257  739.0325730 8739.03257  739.0325730 8739.03257
CCT2       60.73464   60.73464    0.7346439   60.73464    0.7346439   60.73464    0.7346439   60.73464
ALCAM     821.84659  821.84659   21.8465904  821.84659   21.8465904  821.84659   21.8465904  821.84659
EGFR      144.62966  144.62966   44.6296574  144.62966   44.6296574  144.62966   44.6296574  144.62966
DDR1      254.37172  254.37172   54.3717175  254.37172   54.3717175  254.37172   54.3717175  254.37172
RFC2       84.09299   84.09299    4.0929930   84.09299    4.0929930   84.09299    4.0929930   84.09299
HSPA6      57.67287   57.67287    7.6728694   57.67287    7.6728694   57.67287    7.6728694   57.67287
PAX8       78.58733   78.58733   78.8733051   78.58733   78.8733051   78.58733   78.8733051   78.58733
GUCA1A    260.99620  260.99620  200.9962012  260.99620  200.9962012  260.99620  200.9962012  260.99620
UBA7      141.73193  141.73193   41.7319334  141.73193   41.7319334  141.73193   41.7319334  141.73193
THRA      714.82358  714.82358  704.8235783  714.82358  704.8235783  714.82358  704.8235783  714.82358
PTPN21    293.68721  293.68721  293.6872066  293.68721  293.6872066  293.68721  293.6872066  293.68721
CCL5     3242.90209 3242.90209 3242.9020870 3242.90209 3242.9020870 3242.90209 3242.9020870 3242.90209
CYP2E1     57.67287   57.67287   57.6728694   57.67287   57.6728694   57.67287   57.6728694   57.67287
EPHB3      57.67287   57.67287   57.6728694   57.67287   57.6728694   57.67287   57.6728694   57.67287

$hussain
                  1          1          2          2          2          2          1          1
ID          1.00000    2.00000    1.00000    2.00000    1.00000    2.00000    1.00000    2.00000
SLC20A1  3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209
PRDX4     377.81481  377.81481  377.81481  377.81481  377.81481  377.81481  377.81481  377.81481
MCM6      114.88743  114.88743  114.88743  114.88743  114.88743  114.88743  114.88743  114.88743
HEXB     8739.03257 8739.03257 8739.03257 8739.03257 8739.03257 8739.03257 8739.03257 8739.03257
CCT2       60.73464   60.73464   60.73464   60.73464   60.73464   60.73464   60.73464   60.73464
ALCAM     821.84659  821.84659  821.84659  821.84659  821.84659  821.84659  821.84659  821.84659
EGFR      144.62966  144.62966  144.62966  144.62966  144.62966  144.62966  144.62966  144.62966
DDR1      254.37172  254.37172  254.37172  254.37172  254.37172  254.37172  254.37172  254.37172
RFC2       84.09299   84.09299   84.09299   84.09299   84.09299   84.09299   84.09299   84.09299
HSPA6      57.67287   57.67287   57.67287   57.67287   57.67287   57.67287   57.67287   57.67287
PAX8       78.58733   78.58733   78.58733   78.58733   78.58733   78.58733   78.58733   78.58733
GUCA1A    260.99620  260.99620  260.99620  260.99620  260.99620  260.99620  260.99620  260.99620
UBA7      141.73193  141.73193  141.73193  141.73193  141.73193  141.73193  141.73193  141.73193
THRA      714.82358  714.82358  714.82358  714.82358  714.82358  714.82358  714.82358  714.82358
PTPN21    293.68721  293.68721  293.68721  293.68721  293.68721  293.68721  293.68721  293.68721
CCL5     3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209 3242.90209
CYP2E1     57.67287   57.67287   57.67287   57.67287   57.67287   57.67287   57.67287   57.67287
EPHB3      57.67287   57.67287   57.67287   57.67287   57.67287   57.67287   57.67287   57.67287

I run the following code :

testdfQC <- MetaQC(testdf, "c2.cp.biocarta.v5.0.symbols.gmt",
                  filterGenes=FALSE, verbose=TRUE, isParallel=TRUE, nCores=4)

But I get 

Error in { : 
  task 1 failed - "!is.null(d$y) && !is.null(colnames(d$x)) is not TRUE"

No idea what is going wrong. Help appreciated.

r metaqc microarray geneexpression • 743 views
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Entering edit mode

I don't think MetaQC is a Bioconductor package so you should contact its maintainer. 

 

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