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bzguan@ucdavis.edu
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@bzguanucdavisedu-5261
Last seen 10.1 years ago
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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<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>
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<spacingblockx>-1</spacingblockx>
<spacingblocky>-1</spacingblocky>
<numgapsx>0</numgapsx>
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<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>
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</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</extractionalgorithm>
</sentrixdescriptor>