Need help in microarray data analysis
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Entering edit mode
9 weeks ago
rishav513 ▴ 20

Hello all,

Greetings of the day,

I need help with microarray data analysis. This is my workflow

library(affy)
library(affyPLM)
celpath = "/home/sahil/Documents/Microarray"
 data = ReadAffy(celfile.path=celpath)
ph = data@phenoData  #retrieving annotation
ph
An object of class 'AnnotatedDataFrame'
  sampleNames: IR50 3h A.CEL IR50 3h B.CEL ... Nong control C.CEL (18
    total)
  varLabels: sample
  varMetadata: labelDescription


cdfName(data)
[1] "Rice"
length(probeNames(data))
[1] 631066

ph@data
                         sample
IR50 3h A.CEL           IR50 3h A
IR50 3h B.CEL           IR50 3h B
IR50 3h C.CEL           IR50 3h C
IR50 6h A.CEL           IR50 6h A
IR50 6h B.CEL           IR50 6h B
IR50 6h C.CEL           IR50 6h C
IR50 control A.CEL IR50 control A
IR50 control B.CEL IR50 control B
IR50 control C.CEL IR50 control C
Nong 3h A.CEL           Nong 3h A
Nong 3h B.CEL           Nong 3h B
Nong 3h C.CEL           Nong 3h C
Nong 6h A.CEL           Nong 6h A
Nong 6h B.CEL           Nong 6h B
Nong 6h C.CEL           Nong 6h C
Nong control A.CEL Nong control A
Nong control B.CEL Nong control B
Nong control C.CEL Nong control C

but when trying to fit a probe-level model to the data, it is showing an error

Pset = fitPLM(data,output.param=list(varcov="none"))

Error in fitPLM(data, output.param = list(varcov = "none")) : 
  ERROR; return code from pthread_create() is 22
Microarray R • 364 views
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Entering edit mode

Sorry for the disturbance, but I solved it now. Thank you all for your time.

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What was the solution?

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7 weeks ago
rishav513 ▴ 20

I installed preprocessCore disabling threading like this:

BiocManager::install("preprocessCore", configure.args="--disable-threading")
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