Question: The mis-match platform read by bioconductor --> MOE430B
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gravatar for Alex Tsoi
12.0 years ago by
Alex Tsoi260
Alex Tsoi260 wrote:
Dear All, I am wondering how does the bioconductor know what platforms the .cel files come from when reading the raw data by using eg. ReadAffy() or even justGCRMA(). I have several raw .cel files downloaded from GEO, and they are supposed to be from the MOE430B, however, when I used either ReadAffy() or justGCRMA(), I received this error: Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : Cel file /GSM79006.CEL does not seem to be of MOE430A type I tried different samples that also used MOE430B, and each of them gives the same error. The .cel file is similar to this: [CEL] Version=3 [HEADER] Cols=712 Rows=712 TotalX=712 TotalY=712 OffsetX=0 OffsetY=0 GridCornerUL=235 231 GridCornerUR=4506 215 GridCornerLR=4524 4485 GridCornerLL=252 4501 Axis-invertX=0 AxisInvertY=0 swapXY=0 DatHeader=[2..44430] A40200B_++:CLS=4733 RWS=4733 XIN=3 YIN=3 VE=17 2.0 06/24/04 11:23:43 HP MOE430B.1sq 6 .............. As you could see, it specifies MOE430B, but I 'm not sure how the bioconductor figured that this is a MOE430A , and gives the error.. I greatly appreciate for any comment of suggestion. Thanks a lot, Alex- -- Lam C. Tsoi (Alex) Medical University of South Carolina
moe430a moe430b • 398 views
ADD COMMENTlink modified 12.0 years ago by Ben Bolstad1.2k • written 12.0 years ago by Alex Tsoi260
Answer: The mis-match platform read by bioconductor --> MOE430B
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gravatar for Ben Bolstad
12.0 years ago by
Ben Bolstad1.2k
Ben Bolstad1.2k wrote:
At least one of your files purports to be 430A since ReadAffy() gets this information also directly from the CEL files. In particular, it looks at the first CEL file for its type and then checks subsequent CEL files to see if they have this same type. Best, Ben > Dear All, > > I am wondering how does the bioconductor know what platforms the .cel > files come from when reading the raw data by using eg. ReadAffy() or > even justGCRMA(). > > I have several raw .cel files downloaded from GEO, and they are > supposed to be from the MOE430B, however, when I used either > ReadAffy() or justGCRMA(), I received this error: > > Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, > : > Cel file /GSM79006.CEL does not seem to be of MOE430A type > > I tried different samples that also used MOE430B, and each of them > gives the same error. > > The .cel file is similar to this: > > > [CEL] > Version=3 > > [HEADER] > Cols=712 > Rows=712 > TotalX=712 > TotalY=712 > OffsetX=0 > OffsetY=0 > GridCornerUL=235 231 > GridCornerUR=4506 215 > GridCornerLR=4524 4485 > GridCornerLL=252 4501 > Axis-invertX=0 > AxisInvertY=0 > swapXY=0 > DatHeader=[2..44430] A40200B_++:CLS=4733 RWS=4733 XIN=3 YIN=3 VE=17 > 2.0 06/24/04 11:23:43 HP MOE430B.1sq 6 > > .............. > > > As you could see, it specifies MOE430B, but I 'm not sure how the > bioconductor figured that this is a MOE430A , and gives the error.. > > I greatly appreciate for any comment of suggestion. > > Thanks a lot, > Alex- > > -- > Lam C. Tsoi (Alex) > Medical University of South Carolina > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 12.0 years ago by Ben Bolstad1.2k
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