Question: Question on number of probes in CEL and SOFT from GEO
1
gravatar for landscape95
2.8 years ago by
landscape95170
landscape95170 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 • 835 views
ADD COMMENTlink modified 2.8 years ago by theobroma221.1k • written 2.8 years ago by landscape95170
0
gravatar for Sean Davis
2.8 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

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

ADD COMMENTlink written 2.8 years ago by Sean Davis26k
0
gravatar for theobroma22
2.8 years 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 2.8 years ago • written 2.8 years ago by theobroma221.1k
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