Hi.

On Mon, Dec 10, 2012 at 8:49 AM, Hooiveld, Guido <guido.hooiv...@wur.nl> wrote:
> Hi Henrik,
>
>
>
> I am testing the binary CDF files I created for various Gene ST arrays (re:
> discussion last Friday), but I run into problems.
>
> An error is occurring when reading the cell files. According to the change
> log this error has been reported before and should have been fixed by you
> (in version: 2.1.9 [2011-08-31]), so I don’t know why this is happening.
> Could you please have a look?

Thanks for reporting.  It turns out that those CEL files has their
timestamps set to an empty string, which causes the code to break.
I'll fix it.  For now, it's not a serious problem, because you can
tell aroma not to display/query the timestamps by doing:

setOption(aromaSettings, "output/timestampsThreshold", 0L);

That should allow you to do print(cs).

/Henrik

PS. Until your official release, would you mind making the CDF
available to me so I can add redundancy/system tests?  You can send it
offline if you prefer.

>
>
>
> This error occurs when trying to load mouse Gene ST v1.1 arrays; both
> in-house generated files as well as the ones downloaded from Affymetrix
> (http://www.affymetrix.com/support/downloads/demo_data/gene_1_1_st_ap_tissue_sample_data.zip).
> Idem for Affy-provided sample Gene ST v2.1 arrays.
>
> Remarkably, loading Gene ST v1.0 arrays goes fine... (I haven’t tested any
> other array types yet).
>
>
>
> See below for code & output (first STv1.0 (=working); followed by STv1.1
> (=failing)).
>
>
>
> Regards,
>
> Guido
>
>
>
>> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>
>>
>
>
>
>
>
>
>
> # Gene ST v1.0 arrays (working)
>
>> chipType <- "MoGene-1_0-st-v1"
>
>>
>
>> cdf <- AffymetrixCdfFile$byChipType(chipType)
>
>> cdf
>
> AffymetrixCdfFile:
>
> Path: annotationData/chipTypes/MoGene-1_0-st-v1
>
> Filename: MoGene-1_0-st-v1.cdf
>
> File size: 16.69 MB (17500618 bytes)
>
> Chip type: MoGene-1_0-st-v1
>
> RAM: 0.00MB
>
> File format: v4 (binary; XDA)
>
> Dimension: 1050x1050
>
> Number of cells: 1102500
>
> Number of units: 28857
>
> Cells per unit: 38.21
>
> Number of QC units: 0
>
>> cs <- AffymetrixCelSet$byName("guido", cdf=cdf);
>
>> cs
>
> AffymetrixCelSet:
>
> Name: guido
>
> Tags:
>
> Path: rawData/guido/MoGene-1_0-st-v1
>
> Platform: Affymetrix
>
> Chip type: MoGene-1_0-st-v1
>
> Number of arrays: 5
>
> Names: A176_01_MCOLON_CD0_P1, A176_02_MCOLON_CD2_P2, A176_03_MCOLON_CD4_P3,
> A176_04_MCOLON_CD7_P4, A176_05_MCOLON_CD14_P5 [5]
>
> Time period: 2010-01-29 11:45:08 -- 2010-01-29 12:20:51
>
> Total file size: 52.79MB
>
> RAM: 0.01MB
>
>>
>
>
>
> # Check CEL HEADER (using library AffxParser)
>
>> files <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
>
>>   if (length(files) > 0) {
>
> +     header <- readCelHeader(files[1])
>
> +     print(header)
>
> +     rm(header)
>
> +   }
>
> $filename
>
> [1] "./A176_01_MCOLON_CD0_P1.CEL"
>
>
>
> $version
>
> [1] 4
>
>
>
> $cols
>
> [1] 1050
>
>
>
> $rows
>
> [1] 1050
>
>
>
> $total
>
> [1] 1102500
>
>
>
> $algorithm
>
> [1] "Percentile"
>
>
>
> $parameters
>
> [1]
> "Percentile:75;CellMargin:4;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutliersInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExtenstion:1;PoolHeightExtension:1;UseSubgrids:TRUE;RandomizePixels:FALSE;ErrorBasis:StdvMean;StdMult:1.000000;NumDATSubgrids:36"
>
>
>
> $chiptype
>
> [1] "MoGene-1_0-st-v1"
>
>
>
> $header
>
> [1]
> "Cols=1050\nRows=1050\nTotalX=1050\nTotalY=1050\nOffsetX=0\nOffsetY=0\nGridCornerUL=360
> 273\nGridCornerUR=7866 311\nGridCornerLR=7821 7775\nGridCornerLL=315
> 7737\nAxis-invertX=0\nAxisInvertY=0\nswapXY=0\nDatHeader=[1..20525]
> A176_01_mColon_cd0_p1:CLS=8341 RWS=8341 XIN=0  YIN=0  VE=30        2.0
> 01/29/10 11:45:08 50209050  M10   \024  \024 MoGene-1_0-st-v1.1sq \024  \024
> \024  \024  \024 570 \024 25434.212891 \024 3.500000 \024 0.7000 \024
> 3\nAlgorithm=Percentile\nAlgorithmParameters=Percentile:75;CellMargin:4;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutliersInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExtenstion:1;PoolHeightExtension:1;UseSubgrids:TRUE;RandomizePixels:FALSE;ErrorBasis:StdvMean;StdMult:1.000000;NumDATSubgrids:36\n"
>
>
>
> $datheader
>
> [1] "[1..20525]  A176_01_mColon_cd0_p1:CLS=8341 RWS=8341 XIN=0  YIN=0  VE=30
> 2.0 01/29/10 11:45:08 50209050  M10   \024  \024 MoGene-1_0-st-v1.1sq \024
> \024  \024  \024  \024 570 \024 25434.212891 \024 3.500000 \024 0.7000 \024
> 3"
>
>
>
> $librarypackage
>
> [1] ""
>
>
>
> $cellmargin
>
> [1] 4
>
>
>
> $noutliers
>
> [1] 12644
>
>
>
> $nmasked
>
> [1] 0
>
>
>
>>
>
>
>
> #Gene ST V1.1 arrays (fails)
>
>> chipType <- "MoGene-1_1-st-v1"
>
>>
>
>> cdf <- AffymetrixCdfFile$byChipType(chipType)
>
>> cdf
>
> AffymetrixCdfFile:
>
> Path: annotationData/chipTypes/MoGene-1_1-st-v1
>
> Filename: MoGene-1_1-st-v1.cdf
>
> File size: 16.69 MB (17500604 bytes)
>
> Chip type: MoGene-1_1-st-v1
>
> RAM: 0.00MB
>
> File format: v4 (binary; XDA)
>
> Dimension: 1190x990
>
> Number of cells: 1178100
>
> Number of units: 28857
>
> Cells per unit: 40.83
>
> Number of QC units: 0
>
>> cs <- AffymetrixCelSet$byName("guido", cdf=cdf)
>
>> cs
>
> Error in if (hasTimestamp) { : argument is of length zero
>
>>
>
>
>
> # Check CEL HEADER
>
>> files <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
>
>>   if (length(files) > 0) {
>
> +     header <- readCelHeader(files[1])
>
> +     print(header)
>
> +     rm(header)
>
> +   }
>
> $filename
>
> [1] "./G065_A05_02_TW188_344.CEL"
>
>
>
> $version
>
> [1] 1
>
>
>
> $cols
>
> [1] 990
>
>
>
> $rows
>
> [1] 1190
>
>
>
> $total
>
> [1] 1178100
>
>
>
> $algorithm
>
> [1] "HT Image Calibration Cell Generation"
>
>
>
> $parameters
>
> [1]
> "NumPixelsToUse:4;ImageCalibration:TRUE;FeatureExtraction:FALSE;IgnoreShiftRowOutliers:FALSE;FixedCellSize:TRUE;UseSubgrids:FALSE;RandomizePixels:FALSE;ErrorBasis:StdvMean;PercentileSpread:15.000000;StdMult:1.000000;ExtendPoolWidth:2;ExtendPoolHeight:2;OutlierLow:1.004000;OutlierHigh:1.500000;OutlierRatioLowPercentile:55;OutlierRatioHighPercentile:75;CellMargin:2;HalfCellRowsDivisor:5;HalfCellRowsRemainder:4;CellIntensityCalculationType:Percentile;Percentile:75;HighCutoff:2000;LowCutoff:4096;PairCutoff:0.000000;featureRows:174;featureColumns:201;featureWidth:5.000000;featureHeight:5.000000;GridULX:0.000000;GridULY:0.000000;GridURX:989.000000;GridURY:0.000000;GridLRX:989.000000;GridLRY:1189.000000;GridLLX:0.000000;GridLLY:1189.000000"
>
>
>
> $chiptype
>
> [1] "MoGene-1_1-st-v1"
>
>
>
> $header
>
> [1] ""
>
>
>
> $datheader
>
> [1] ""
>
>
>
> $librarypackage
>
> [1] "Expression"
>
>
>
> $cellmargin
>
> [1] 2
>
>
>
> $noutliers
>
> [1] 0
>
>
>
> $nmasked
>
> [1] 0
>
>
>
>>
>
>> sessionInfo()
>
> R Under development (unstable) (2012-11-21 r61136)
>
> Platform: i386-w64-mingw32/i386 (32-bit)
>
>
>
> locale:
>
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252
>
> [4] LC_NUMERIC=C                           LC_TIME=English_United
> States.1252
>
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
>
> other attached packages:
>
> [1] aroma.affymetrix_2.7.0 affxparser_1.31.1      aroma.apd_0.2.3
> R.huge_0.4.1           aroma.light_1.29.0
>
>  [6] aroma.core_2.7.1       matrixStats_0.6.2      R.rsp_0.8.2
> R.devices_2.1.3        R.cache_0.6.5
>
> [11] R.filesets_1.6.0       digest_0.6.0           R.utils_1.18.0
> R.oo_1.11.3            R.methodsS3_1.4.2
>
>
>
> loaded via a namespace (and not attached):
>
> [1] PSCBS_0.30.0
>
>>
>
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/

-- 
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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