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fix issue with file
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r4babs2/week-2/workshop.qmd

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@@ -453,9 +453,9 @@ line that describes this relationship so we can use it to estimate the
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molecular weights of other proteins in the gel.
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We will use this gel image (@fig-gel) as an example:
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[26C-10-Coomassie-Blue.jpg](data-image/26C-10-Coomassie-Blue.jpg). This
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gel has two sets of results (one each side) -- since only 4 lanes were
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for each practical group, we put two groups on one gel.
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[sds-page-gel.jpg](data-image/sds-page-gel.jpg). This gel has two sets
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of results (one each side) -- since only 4 lanes were for each practical
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group, we put two groups on one gel.
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- Lane 1 (and 10) is the protein ladder which are the proteins of
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known molecular weights.
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# import gel
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library(imager)
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gel <- load.image("data-image/26C-10-Coomassie-Blue.jpg")
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gel <- load.image("data-image/sds-page-gel.jpg")
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gel_cropped <- crop.borders(gel, nx = 300, ny = 150)
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gel_top <- 180
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gel_bottom <- 990
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pos_patB <- 394
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```
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: :: {fig-gel}
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::: {fig-gel}
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```{r}
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#| echo: false
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#| message: false
@@ -526,7 +525,6 @@ be measured from the top of the gel. These distances and the molecular
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weights of the marker proteins are used to create a standard curve that
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allows us to estimate the molecular weight of ShPatB from its position
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on the gel.
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:::
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We will cover two options:
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You have a file containing the molecular weights of the marker proteins
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[standard-mw.txt](data-image/standard-mw.txt) and the image of the gel
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[26C-10-Coomassie-Blue.jpg](data-image/26C-10-Coomassie-Blue.jpg). The
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molecular weights of the marker proteins are in kilodaltons (kDa)
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[sds-page-gel.jpg](data-image/sds-page-gel.jpg). The molecular weights
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of the marker proteins are in kilodaltons (kDa)
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![](images/do_in_R.png) Make a folder call `data-image` and save
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[standard-mw.txt](data-image/standard-mw.txt) and
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[26C-10-Coomassie-Blue.jpg](data-image/26C-10-Coomassie-Blue.jpg) to it
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[sds-page-gel.jpg](data-image/sds-page-gel.jpg) to it
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![](images/do_in_R.png) Imort the molecular weights of the marker
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proteins from [standard-mw.txt](data-image/standard-mw.txt)
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![](images/do_in_R.png) Import the gel image:
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```{r}
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gel <- load.image("data-image/26C-10-Coomassie-Blue.jpg")
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gel <- load.image("data-image/sds-page-gel.jpg")
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```
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Base R's generic `plot()` function can handle image files and plot axes

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