[BioC] Affy : CDF problems

[Girardot Fabrice]

Hi !
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I am trying to reanalyze the data from de Gregorio et al. (http://www.fruit=
fly.org/expression/immunity/) using the affy package, wich I have already s=
uccessfully used with some other datasets. However I am encountering a stra=
nge problem here. ReadAffy seems to have a problem with 4 of the 34 chips o=
f the set.
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Here is the error message for the four chips :
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> test <- ReadAffy(widget =3D TRUE)
Warning messages:=20
1: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compr=
ess =3D compress)=20
2: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compr=
ess =3D compress)=20
3: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compr=
ess =3D compress)=20
4: could not find CDF name, setting it to 'unknown' in: whatcdf(file, compr=
ess =3D compress)=20

When I manually open the files I don't see any difference between the 'good=
' and the 'bad' files :
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a good file's headers :
[CEL]
Version=3D3
[HEADER]
Cols=3D640
Rows=3D640
TotalX=3D640
TotalY=3D640
OffsetX=3D0
OffsetY=3D0
GridCornerUL=3D226 233
GridCornerUR=3D4488 233
GridCornerLR=3D4488 4498
GridCornerLL=3D227 4499
Axis-invertX=3D0
AxisInvertY=3D0
swapXY=3D0
DatHeader=3D[39..46276]  bacterial infection t0 array1:CLS=3D4733 RWS=3D473=
3 XIN=3D3  YIN=3D3  VE=3D17        2.0 02/20/ 1 12:23:18    =14 GridVerify=
=3DNone =14 DrosGenome1.1sq =14  =14  =14  =14  =14  =14  =14  =14  =14 6
Algorithm=3DPercentile
AlgorithmParameters=3DPercentile:75;CellMargin:2;OutlierHigh:1.500;OutlierL=
ow:1.004
[INTENSITY]
NumberCells=3D409600
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The same for a 'bad' file :
[CEL]
Version=3D3
[HEADER]
Cols=3D640
Rows=3D640
TotalX=3D640
TotalY=3D640
OffsetX=3D0
OffsetY=3D0
GridCornerUL=3D225 234
GridCornerUR=3D4488 240
GridCornerLR=3D4482 4505
GridCornerLL=3D220 4500
Axis-invertX=3D0
AxisInvertY=3D0
swapXY=3D0
DatHeader=3D[49..46275]  bacterial infection t0 array2 scan2:CLS=3D4733 RWS=
=3D4733 XIN=3D3  YIN=3D3  VE=3D17        2.0 02/20/ 1 16:05:31    =14 GridV=
erify=3DNone =14 DrosGenome1.1sq =14  =14  =14  =14  =14  =14  =14  =14  =
=14 6
Algorithm=3DPercentile
AlgorithmParameters=3DPercentile:75;CellMargin:2;OutlierHigh:1.500;OutlierL=
ow:1.004
[INTENSITY]
NumberCells=3D409600
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Quite logically, justRMA is just as confused with those files. Youcan downl=
oad some the CEL files at the following address : http://134.59.90.101/chip=
s/chips.htm
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Any advice, question, explanation would be more than welcome !
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--
Fabrice Girardot
Equipe Biologie Virtuelle
UMR 6543
Nice, France



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