CHP and CEL file

Question

[R]

Hello everyone: I download a microarray row data "GSE6990_RAW" (affymetrix) that contains CHP and CEL files. (In my previous analysis the raw data contained only CEL files.) I don't know what software to use for analysis this data (I cannot analyze this data by Expression Console software)

Answer 1

[Kevin Blighe]

The GEO record for the study indicates that the authors used GeneSpring GX 7.3; however, this is a commercial program.

You can just re-process the data in R, like this:

require(affy)
require(barley1cdf)

list.files('.', pattern = '*.[Cc]EL$')
 [1] "GSM160464.CEL" "GSM160744.CEL" "GSM160815.CEL" "GSM160819.CEL"
 [5] "GSM160822.CEL" "GSM160823.CEL" "GSM160826.CEL" "GSM160831.CEL"
 [9] "GSM161148.CEL" "GSM261519.CEL" "GSM261520.CEL"

data <- ReadAffy(filenames = list.files('.', pattern = '*.[Cc]EL$'))

eset <- rma(data)
Background correcting
Normalizing
Calculating Expression

eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22840 features, 11 samples 
  element names: exprs 
protocolData
  sampleNames: GSM160464.CEL GSM160744.CEL ... GSM261520.CEL (11 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: GSM160464.CEL GSM160744.CEL ... GSM261520.CEL (11 total)
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: barley1 

par(mar = c(10,2,2,2))
boxplot(exprs(eset), notch = TRUE, col = 'forestgreen', las = 2)

-------------------

They also provide CHP files; however, I would just ignore those. If you do want to look at the data in the CHP files, then use readChp

str(affxparser::readChp('GSM160744.CHP'))
List of 7
 $ FileId               : chr ""
 $ AlgorithmName        : chr "ExpressionStat"
 $ AlgorithmVersion     : chr "5.0"
 $ ArrayType            : chr "Barley1"
 $ AlgorithmParameters  :List of 13
  ..$ SFGene      : chr "All"
  ..$ SF          : chr "1.705831"
  ..$ NF          : chr "1.000000"
  ..$ TGT         : chr "500"
  ..$ Perturbation: chr "1.1"
  ..$ Gamma2L     : chr "0.006"
  ..$ Gamma2H     : chr "0.006"
  ..$ Gamma1L     : chr "0.0045"
  ..$ Gamma1H     : chr "0.0045"
  ..$ Tau         : chr "0.015"
  ..$ Alpha2      : chr "0.065"
  ..$ Alpha1      : chr "0.05"
  ..$ BF          : chr ""
 $ SummaryParameters    :List of 16
  ..$ SFGene      : chr "All"
  ..$ SF          : chr "1.705831"
  ..$ NF          : chr "1.000000"
  ..$ TGT         : chr "500"
  ..$ Perturbation: chr "1.1"
  ..$ Gamma2L     : chr "0.006"
  ..$ Gamma2H     : chr "0.006"
  ..$ Gamma1L     : chr "0.0045"
  ..$ Gamma1H     : chr "0.0045"
  ..$ Tau         : chr "0.015"
  ..$ Alpha2      : chr "0.065"
  ..$ Alpha1      : chr "0.05"
  ..$ BF          : chr ""
  ..$ RawQ        : chr "2.97"
  ..$ Noise       : chr "Avg:3.84,Stdev:0.43,Max:5.1,Min:3.1"
  ..$ Background  : chr "Avg:71.51,Stdev:2.48,Max:76.7,Min:66.3"
 $ QuantificationEntries:List of 12
  ..$ DetectionPValue   : num [1:22840] 0.04296 0.00202 0.005 0.0011 0.00141 ...
  ..$ Signal            : num [1:22840] 239 136 122 377 268 ...
  ..$ NumPairs          : int [1:22840] 20 20 20 20 20 20 20 20 20 20 ...
  ..$ NumUsedPairs      : int [1:22840] 20 20 20 20 20 20 20 20 20 20 ...
  ..$ Detection         : int [1:22840] 0 0 0 0 0 0 0 0 0 2 ...
  ..$ HasCompResults    : logi [1:22840] FALSE FALSE FALSE FALSE FALSE FALSE ...
  ..$ ChangePValue      : num [1:22840] 1.09e-08 1.26e-44 1.68e-44 1.54e-44 6.87e-44 ...
  ..$ SignalLogRatio    : num [1:22840] 2.62e-12 0.00 0.00 0.00 0.00 ...
  ..$ SignalLogRatioLow : num [1:22840] 9.47e-04 5.99e-02 4.54e+24 4.54e+24 6.87e-44 ...
  ..$ SignalLogRatioHigh: num [1:22840] 1.04e-05 2.56e-09 6.88e-10 6.88e-10 0.00 ...
  ..$ NumCommonPairs    : int [1:22840] 19756 53 12334 12334 49 11824 49 55 55 19756 ...
  ..$ Change            : int [1:22840] 105 97 54 53 48 48 48 48 105 105 ...

Kevin