User: Joseph Barry

gravatar for Joseph Barry
Joseph Barry160
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160
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Location:
Dana-Farber Cancer Institute, Boston, USA
Last seen:
3 years ago
Joined:
8 years ago
Email:
j***********@embl.de

Posts by Joseph Barry

<prev • 31 results • page 1 of 4 • next >
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Answer: A: cellHTS2 importa and analysing data from chemical compound screening
... As long as the columns 'Filename', 'Plate', and 'Replicate' are there, I don't think it matters. I'd probably choose to make 'Condition' the fourth column. See the Details section of ?readPlateList for more information. 'Condition' is really an optional column, which is why it's not included in the ...
written 3.0 years ago by Joseph Barry160
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Answer: A: cellHTS2 importa and analysing data from chemical compound screening
... Dear Andreia, Thanks for your questions. 1) First please check that the platelist file is a tab delimited file, with \t separating fields rather than a space. This is detailed in the help to the readPlateList function. This might explain your read-in issue. Second, it's unclear if you specify a " ...
written 3.0 years ago by Joseph Barry160
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Answer: A: EBImage readImage hangs when reading tif file with multiple frames.
... Hi Kristina, I can open it fine with the following. The read-in only takes a few seconds. > library(EBImage) > x <- readImage("DAPI_Mask.tif") > dim(x) [1] 1024 1024 145 I'm using linux (Fedora). At least in principle that shouldn't matter though. Can you post sessionInfo()? Is your ...
written 3.6 years ago by Joseph Barry160
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Answer: A: cellHTS2 configure error
... There's a high chance that your error is due to formatting problems in your plateConf file. Please try to read in the plateConf file directly using read.table("PlateConf.txt", sep="\t", header=TRUE, as.is=TRUE, na.strings="", fill=TRUE, skip=2) You should see a table with your three columns: Plate ...
written 3.8 years ago by Joseph Barry160
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Answer: A: cellHTS2 configure error
... Hi Eduardo, Thanks for posting this. Just to let you know that I've recreated the error locally and am working towards a solution. ...
written 3.8 years ago by Joseph Barry160
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Answer: A: Web CellHTS2 data upload
... First it is important to know that web cellHTS2 is an independent project from the Bioconductor cellHTS2 package. Therefore I cannot help you directly if the problem is due to the web cellHTS2 server (I'm not even sure who the admin is for web cellHTS2 right now). You could try using the base cellHT ...
written 3.9 years ago by Joseph Barry160
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Answer: A: cellHTS2 : negative values after normalization
... Hi, you are right to be untrusting of these ratios. As your data is now on a log-scale, you should now be looking at differences from your controls i.e. x_i - mean(x_controlPos). This is because of the mathematical properties of logarithms, since log(x/y)=log(x)-log(y). ...
written 4.3 years ago by Joseph Barry160
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Comment: C: B-Score problems with CellHTS2
... Are the controls in the border columns all the same, or do you expect to see a particular ranking due to e.g. a  concentration gradient? At this point you're looking for any evidence that the experiment is indeed working as expected. If your design is such that you require a high signal within the ...
written 4.3 years ago by Joseph Barry160
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Comment: C: B-Score problems with CellHTS2
... For information about the locfit correction method please see the help documentation about normalization methods  by typing ?normalizePlates in R. A lot of this comes down to the layout of compounds on the plate. If your assay is prone to spatial bias on the plates, it might be that you should not p ...
written 4.3 years ago by Joseph Barry160
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Answer: A: B-Score problems with CellHTS2
... Hi zmorehouse, (i) are your strongest inhibitors showing a more expected ranking in your hitlist if you do either no normalization or one that does no spatial correction (e.g. method="median" in normalizePlates)? (ii) does the raw data show 'stripes' of true signal, where particular rows or column ...
written 4.3 years ago by Joseph Barry160

Latest awards to Joseph Barry

Popular Question 3.0 years ago, created a question with more than 1,000 views. For converting UniProt to SGD ids using UniProt.wd
Scholar 4.3 years ago, created an answer that has been accepted. For A: B-Score problems with CellHTS2

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