[BioC] beadarray package: question about processSwathData() segmentHeight and segmentWidth values
bzguan at ucdavis.edu
bzguan at ucdavis.edu
Tue May 1 09:48:27 CEST 2012
Hi,
I have data from Human660W_quad beadchips generated by Illumina iScan and am trying to run the
processSwathData function to deconvolute the bead-level data. I am not sure what to put for the
values for the segmentHeight and segmentWidth. I tried looking for these two values in the .sdf file
but there are a few different values of height and width listed in the .sdf file. I wasn't sure which
values to use, so I tried two sets of values for segmentHeight and segmentWidth and both sets of
values worked, which made me uncertain as to which set of values I should use. I have included the
.sdf file below. I am interested in figuring out which values listed in the .sdf file I should use for
the segmentHeight and segmentWidth in the processSwathData function.
processSwathData(inputDir = "/Users/Desktop/", outputDir="/Users/Desktop/",
segmentHeight=460,segmentWidth=460,verbose=TRUE)
processSwathData(inputDir = "/Users/Desktop/", outputDir="/Users/Desktop/",
segmentHeight=1950,segmentWidth=7300,verbose=TRUE)
Thanks in advance for any suggestions,
Anna
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<Indices>
<int>0</int>
<int>2</int>
</Indices>
</SparseMapSet>
<SparseMapSet>
<Indices>
<int>1</int>
<int>3</int>
</Indices>
</SparseMapSet>
<SparseMapSet>
<Indices>
<int>11</int>
<int>9</int>
</Indices>
</SparseMapSet>
</Sets>
</SparseMapGroup>
</MapGroups>
<SampleImagingOrder>
<int>0</int>
<int>1</int>
<int>2</int>
<int>3</int>
</SampleImagingOrder>
<SectionImagingOrder>
<int>0</int>
<int>1</int>
<int>2</int>
<int>3</int>
<int>4</int>
<int>5</int>
<int>6</int>
<int>7</int>
<int>8</int>
<int>9</int>
<int>10</int>
<int>11</int>
</SectionImagingOrder>
</AnalyticalMapping>
<AnalyticalTiltMapping>
<InvertImageXAxis>false</InvertImageXAxis>
<MarkerWidth>0</MarkerWidth>
<MarkerHeight>0</MarkerHeight>
</AnalyticalTiltMapping>
<DecodeImagingProperties>
<Resolution>0</Resolution>
<FieldOfView>
<Width>0</Width>
<Height>0</Height>
</FieldOfView>
</DecodeImagingProperties>
<ManufacturingProperties>
<FlowCell>ILD</FlowCell>
<PartNumber>11286817</PartNumber>
<Rev>A</Rev>
<Description>207829_207837_4X3Q</Description>
<Platform>ILD</Platform>
<Type>Slide</Type>
</ManufacturingProperties>
<AnalyticalImagingProperties>
<Resolution>1</Resolution>
<FieldOfView>
<Width>7300</Width>
<Height>1950</Height>
</FieldOfView>
</AnalyticalImagingProperties>
<SectionsPerSuperSection>4</SectionsPerSuperSection>
<AutoFocusOnEachSection>true</AutoFocusOnEachSection>
<RegistrationParameters>
<NumCores>1051253</NumCores>
<NumSubGridSymmetryAxes>3</NumSubGridSymmetryAxes>
<NumGridSymmetryAxes>2</NumGridSymmetryAxes>
<NumBlockSymmetryAxes>2</NumBlockSymmetryAxes>
<NumVerticalStripes>1</NumVerticalStripes>
<SizeSubgridX>1</SizeSubgridX>
<SizeSubgridY>1</SizeSubgridY>
<SizeGridX>1901</SizeGridX>
<SizeGridY>553</SizeGridY>
<SpacingGridX>-1</SpacingGridX>
<SpacingGridY>-1</SpacingGridY>
<Angle>-1000</Angle>
<SizeBlockX>1</SizeBlockX>
<SizeBlockY>1</SizeBlockY>
<SpacingBlockX>-1</SpacingBlockX>
<SpacingBlockY>-1</SpacingBlockY>
<NumGapsX>0</NumGapsX>
<NumGapsY>0</NumGapsY>
<SizeGapX>3</SizeGapX>
<SizeGapY>3</SizeGapY>
<Version>2</Version>
<InvertJaggedEdge>false</InvertJaggedEdge>
</RegistrationParameters>
<SectionLabels>
<string>1</string>
<string>2</string>
<string>3</string>
<string>4</string>
<string>5</string>
<string>6</string>
<string>7</string>
<string>8</string>
<string>9</string>
<string>10</string>
<string>11</string>
<string>12</string>
</SectionLabels>
<SampleLabels>
<string>R01C01</string>
<string>R02C01</string>
<string>R01C02</string>
<string>R02C02</string>
</SampleLabels>
<Name>BeadChip 4x3Q</Name>
<Comment />
<Class>Slide</Class>
<AssayType>Infinium HD</AssayType>
<Path />
<RegistrationAlgorithmName>StandardGeneric</RegistrationAlgorithmName>
<ExtractionAlgorithmName>StandardWithBackground</ExtractionAlgorithmName>
</SentrixDescriptor>
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