Hi Anna,

My apologies, I thought I'd got round to automating this step, as I agree
that the values are not obvious at all.  The sdf values that are supposed
to correspond to those two arguments are :

<SizeGridX>1901</SizeGridX>
<SizeGridY>553</SizeGridY>

with segmentHeight = SizeGridX and segmentWidth = SizeGridY.  Why I hadn't
put that in the manual I have no idea, but it's in there now.

I haven't ever seen data from the Human660W_quad chip, but assuming it is
scanned in the same way (two side-by-side images with a small overlap),
then I think those values should work.  Let me know if it looks like it
hasn't.

Mike Smith

On 1 May 2012 08:48, <bzguan@ucdavis.edu> wrote:

>
> 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
>
>
>
>
> <?xml version="1.0" encoding="utf-8"?>
> <SentrixDescriptor xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> xmlns:xsd="http://www.w3.org/2001/XMLSchema">
>  <PhysicalProperties>
>    <PhysicalWidth>25000</PhysicalWidth>
>    <PhysicalHeight>82500</PhysicalHeight>
>    <SectionWidth>7034</SectionWidth>
>    <SectionHeight>1771</SectionHeight>
>    <SampleWidth>8009</SampleWidth>
>    <SampleHeight>27837</SampleHeight>
>    <DecodeMarkerOffset>
>      <X>4017</X>
>      <Y>-135</Y>
>    </DecodeMarkerOffset>
>    <SamplePositions>
>      <RelativeXYZPoint>
>        <X>7833</X>
>        <Y>19157</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>7833</X>
>        <Y>47510</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>17167</X>
>        <Y>19157</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>17167</X>
>        <Y>47510</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>    </SamplePositions>
>    <SectionPositions>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>-12152</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>-10351</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>-8550</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>-6749</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>-2701</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>-900</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>901</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>2702</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>6750</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>8551</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>10352</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>12153</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>    </SectionPositions>
>    <DecodeSectionPositions>
>      <RelativeXYZPoint>
>        <X>0</X>
>        <Y>0</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>    </DecodeSectionPositions>
>    <DecodeMarkerLocations>
>      <RelativeXYZPoint>
>        <X>3816</X>
>        <Y>6885</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>11850</X>
>        <Y>6885</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>
>      <RelativeXYZPoint>
>        <X>3816</X>
>        <Y>16336</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>11850</X>
>        <Y>16336</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>
>      <RelativeXYZPoint>
>        <X>3816</X>
>        <Y>25787</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>11850</X>
>        <Y>25787</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>
>      <RelativeXYZPoint>
>        <X>3816</X>
>        <Y>35238</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>11850</X>
>        <Y>35238</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>
>      <RelativeXYZPoint>
>        <X>3816</X>
>        <Y>44689</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>11850</X>
>        <Y>44689</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>
>      <RelativeXYZPoint>
>        <X>3816</X>
>        <Y>54140</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>11850</X>
>        <Y>54140</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>
>      <RelativeXYZPoint>
>        <X>13150</X>
>        <Y>6885</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>21184</X>
>        <Y>6885</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>
>      <RelativeXYZPoint>
>        <X>13150</X>
>        <Y>16336</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>21184</X>
>        <Y>16336</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>
>      <RelativeXYZPoint>
>        <X>13150</X>
>        <Y>25787</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>21184</X>
>        <Y>25787</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>
>      <RelativeXYZPoint>
>        <X>13150</X>
>        <Y>35238</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>21184</X>
>        <Y>35238</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>
>      <RelativeXYZPoint>
>        <X>13150</X>
>        <Y>44689</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>21184</X>
>        <Y>44689</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>
>      <RelativeXYZPoint>
>        <X>13150</X>
>        <Y>54140</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>21184</X>
>        <Y>54140</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>    </DecodeMarkerLocations>
>    <AnalyticalMarkerLocations>
>      <RelativeXYZPoint>
>        <X>1328</X>
>        <Y>9706</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>23672</X>
>        <Y>9706</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>1328</X>
>        <Y>19157</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>23672</X>
>        <Y>19157</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>1328</X>
>        <Y>28608</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>23672</X>
>        <Y>28608</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>1328</X>
>        <Y>38059</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>23672</X>
>        <Y>38059</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>1328</X>
>        <Y>47510</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>23672</X>
>        <Y>47510</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>1328</X>
>        <Y>56961</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>      <RelativeXYZPoint>
>        <X>23672</X>
>        <Y>56961</Y>
>        <Z>0</Z>
>      </RelativeXYZPoint>
>    </AnalyticalMarkerLocations>
>  </PhysicalProperties>
>  <UIProperties>
>    <SectionScale>0.06362036</SectionScale>
>    <SampleScale>0.337418169</SampleScale>
>    <SectionColor>
>      <R>255</R>
>      <G>255</G>
>      <B>224</B>
>    </SectionColor>
>    <SampleColor>
>      <R>110</R>
>      <G>120</G>
>      <B>140</B>
>    </SampleColor>
>    <SubstrateColor>
>      <R>29</R>
>      <G>46</G>
>      <B>63</B>
>    </SubstrateColor>
>    <LabelPos>
>      <X>0</X>
>      <Y>0.45</Y>
>    </LabelPos>
>    <SampleHighlightColor>
>      <R>255</R>
>      <G>0</G>
>      <B>0</B>
>    </SampleHighlightColor>
>    <SectionHighlightColor>
>      <R>255</R>
>      <G>0</G>
>      <B>0</B>
>    </SectionHighlightColor>
>    <LabelColor>
>      <R>29</R>
>      <G>46</G>
>      <B>63</B>
>    </LabelColor>
>    <LabelFontColor>
>      <R>245</R>
>      <G>245</G>
>      <B>245</B>
>    </LabelFontColor>
>    <SampleLocations>
>      <NormalizedPoint>
>        <X>-0.0565697</X>
>        <Y>-0.267793924</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>-0.0565697</X>
>        <Y>0.0758788</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0.0565697</X>
>        <Y>-0.267793924</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0.0565697</X>
>        <Y>0.0758788</Y>
>      </NormalizedPoint>
>    </SampleLocations>
>    <SectionLocations>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>-0.436541284</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>-0.371843222</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>-0.307145160</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>-0.242447097</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>-0.097029132</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>-0.032331069</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>0.0323669929</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>0.0970650552</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>0.2424830209</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>0.3071810832</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>0.3718791455</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>0.4365772078</Y>
>      </NormalizedPoint>
>    </SectionLocations>
>    <DecodeSectionLocations>
>      <NormalizedPoint>
>        <X>0</X>
>        <Y>0</Y>
>      </NormalizedPoint>
>    </DecodeSectionLocations>
>    <DecodeMarkers>
>      <MarkerType>
>        <Location>
>          <X>-0.105260611</X>
>          <Y>-0.416545451</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>-0.007878789</X>
>          <Y>-0.416545451</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>
>      <MarkerType>
>        <Location>
>          <X>-0.105260611</X>
>          <Y>-0.3019879</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>-0.007878789</X>
>          <Y>-0.3019879</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>
>      <MarkerType>
>        <Location>
>          <X>-0.105260611</X>
>          <Y>-0.187430292</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>-0.007878789</X>
>          <Y>-0.187430292</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>
>      <MarkerType>
>        <Location>
>          <X>-0.105260611</X>
>          <Y>-0.07287271</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>-0.007878789</X>
>          <Y>-0.07287271</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>
>      <MarkerType>
>        <Location>
>          <X>-0.105260611</X>
>          <Y>0.0416848622</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>-0.007878789</X>
>          <Y>0.0416848622</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>
>      <MarkerType>
>        <Location>
>          <X>-0.105260611</X>
>          <Y>0.156242445</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>-0.007878789</X>
>          <Y>0.156242445</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>
>      <MarkerType>
>        <Location>
>          <X>0.007878787</X>
>          <Y>-0.416545451</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.105260611</X>
>          <Y>-0.416545451</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>
>      <MarkerType>
>        <Location>
>          <X>0.007878787</X>
>          <Y>-0.3019879</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.105260611</X>
>          <Y>-0.3019879</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>
>      <MarkerType>
>        <Location>
>          <X>0.007878787</X>
>          <Y>-0.187430292</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.105260611</X>
>          <Y>-0.187430292</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>
>      <MarkerType>
>        <Location>
>          <X>0.007878787</X>
>          <Y>-0.07287271</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.105260611</X>
>          <Y>-0.07287271</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>
>      <MarkerType>
>        <Location>
>          <X>0.007878787</X>
>          <Y>0.0416848622</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.105260611</X>
>          <Y>0.0416848622</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>
>      <MarkerType>
>        <Location>
>          <X>0.007878787</X>
>          <Y>0.156242445</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.105260611</X>
>          <Y>0.156242445</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>    </DecodeMarkers>
>    <AnalyticalMarkers>
>      <MarkerType>
>        <Location>
>          <X>-0.135418192</X>
>          <Y>-0.382351518</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.135418192</X>
>          <Y>-0.382351518</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>-0.135418192</X>
>          <Y>-0.267793924</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.135418192</X>
>          <Y>-0.267793924</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>-0.135418192</X>
>          <Y>-0.153236359</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.135418192</X>
>          <Y>-0.153236359</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>-0.135418192</X>
>          <Y>-0.0386787765</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.135418192</X>
>          <Y>-0.0386787765</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>-0.135418192</X>
>          <Y>0.0758788</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.135418192</X>
>          <Y>0.0758788</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>-0.135418192</X>
>          <Y>0.190436378</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>      <MarkerType>
>        <Location>
>          <X>0.135418192</X>
>          <Y>0.190436378</Y>
>        </Location>
>        <Type>Slide</Type>
>        <SampleIndex>0</SampleIndex>
>      </MarkerType>
>    </AnalyticalMarkers>
>    <SubstrateBorder>
>      <NormalizedPoint>
>        <X>-0.151515156</X>
>        <Y>-0.5</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0.151515156</X>
>        <Y>-0.5</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0.151515156</X>
>        <Y>0.5</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>-0.151515156</X>
>        <Y>0.5</Y>
>      </NormalizedPoint>
>    </SubstrateBorder>
>    <SampleBorder>
>      <NormalizedPoint>
>        <X>-0.1438553</X>
>        <Y>-0.50000006</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0.1438553</X>
>        <Y>-0.50000006</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>0.1438553</X>
>        <Y>0.50000006</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>-0.1438553</X>
>        <Y>0.50000006</Y>
>      </NormalizedPoint>
>    </SampleBorder>
>    <SectionBorder>
>      <NormalizedPoint>
>        <X>-1.98588371</X>
>        <Y>-0.5</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>1.98588371</X>
>        <Y>-0.5</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>1.98588371</X>
>        <Y>0.5</Y>
>      </NormalizedPoint>
>      <NormalizedPoint>
>        <X>-1.98588371</X>
>        <Y>0.5</Y>
>      </NormalizedPoint>
>    </SectionBorder>
>    <MatrixTags />
>  </UIProperties>
>  <DecodeMapping>
>    <InvertImageXAxis>false</InvertImageXAxis>
>    <AutocenterAlignmentAlgorithm>OdysseyII</AutocenterAlignmentAlgorithm>
>    <MarkerWidth>460</MarkerWidth>
>    <MarkerHeight>460</MarkerHeight>
>    <MappingGroupForSample>
>      <int>0</int>
>      <int>0</int>
>      <int>0</int>
>      <int>0</int>
>    </MappingGroupForSample>
>    <MappingGroupBySection>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>      <string>0</string>
>    </MappingGroupBySection>
>    <MapGroups>
>      <SparseMapGroup>
>        <Sets>
>          <SparseMapSet>
>            <Indices>
>              <int>0</int>
>            </Indices>
>          </SparseMapSet>
>          <SparseMapSet>
>            <Indices>
>              <int>13</int>
>            </Indices>
>          </SparseMapSet>
>          <SparseMapSet>
>            <Indices>
>              <int>10</int>
>            </Indices>
>          </SparseMapSet>
>          <SparseMapSet>
>            <Indices>
>              <int>23</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>
>  </DecodeMapping>
>  <AnalyticalMapping>
>    <InvertImageXAxis>true</InvertImageXAxis>
>    <AutocenterAlignmentAlgorithm>OdysseyII</AutocenterAlignmentAlgorithm>
>    <MarkerWidth>85</MarkerWidth>
>    <MarkerHeight>90</MarkerHeight>
>    <MappingGroupForSample>
>      <int>0</int>
>      <int>0</int>
>      <int>0</int>
>      <int>0</int>
>    </MappingGroupForSample>
>    <MapGroups>
>      <SparseMapGroup>
>        <Sets>
>          <SparseMapSet>
>            <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>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

	[[alternative HTML version deleted]]

