Question: Question on number of probes in CEL and SOFT from GEO
1
gravatar for landscape95
22 months ago by
landscape95160
landscape95160 wrote:

Hello everyone, I wonder why there is a different between the number of probes after I process the data from GEO in CEL compared to SOFT files. For example, data set GSM272923 just have 18382 probes as described in the table near the end of the page while as I downloaded CEL file, there were 54675 probes?

Your help would be really appreciated!

Dataset GSM272923 from GSE10810: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM272923

My code to process the CEL files:

  RAWstr = "GSE10810_RAW.tar"
  RAWdirectory = paste("./RAWsets", substr(RAWstr, 1, nchar(RAWstr) - 8), sep = "/")
  tardir = paste("./RAWsets", RAWstr, sep = "/")
  untar(tardir, exdir = RAWdirectory, verbose = F)
  cels = list.files(RAWdirectory, pattern = "CEL.gz", full.names = T)
  sapply(cels, gunzip)
  data.raw = ReadAffy(filenames = substr(cels, 1, nchar(cels)-3), verbose = F, cdfname = "hgu133plus2cdf")
  data.matrix = rma(data.raw)
  tmp = exprs(data.matrix)
geo • 648 views
ADD COMMENTlink modified 22 months ago by theobroma221.1k • written 22 months ago by landscape95160
0
gravatar for Sean Davis
22 months ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

The original submitters apparently filtered the data. That is not uncommon.

ADD COMMENTlink written 22 months ago by Sean Davis25k
0
gravatar for theobroma22
22 months ago by
theobroma221.1k
theobroma221.1k wrote:

Those 18K probes could be the result of significance tests between a P-value of 0-1, and may included duplicated probes.

The paper should clue you into your questions, like what is contained in the M&M section.

ADD COMMENTlink modified 22 months ago • written 22 months ago by theobroma221.1k
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