User: Joseph Barry

gravatar for Joseph Barry
Joseph Barry160
Reputation:
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 2 of 4 • next >
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Answer: A: Failed to annotated my wells
... An update to the thread for completeness. User wstoo1 sent me an example dataset privately. We figured out that he was assuming that the 'wellAnno' column should contain gene identifiers, which is not a valid expectation. The 'wellAnno' column contains information about the control status of differe ...
written 4.3 years ago by Joseph Barry160
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Comment: C: Failed to annotated my wells
... Okay, at this point it is hard for me to pinpoint the problem without seeing the data. Would you mind privately sending me example data?  joseph.barry@... please get the rest from my user profile ...
written 4.4 years ago by Joseph Barry160
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Answer: A: Failed to annotated my wells
... Great, so the annotate function is working. Can you try moving the annotation step to earlier in your pipeline e.g. after configure. The annotation will get carried along. Try running state(x) state(xnp) state(xf) and so on to follow what objects have been properly annotated. Since xf comes later ...
written 4.4 years ago by Joseph Barry160
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Comment: C: Failed to annotated my wells
... Unfortunately you just sharing the script your supervisor sent you does not give me the information I need to ascertain whether or not the annotate function worked. Please wrap the annotate command with the following 'fData' command, as I suggested in my previous post. head(fData(xf)) xfw<-annot ...
written 4.4 years ago by Joseph Barry160
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Answer: A: Failed to annotated my wells
... Hi, Can you print the feature data before and after the annotate step to clarify whether or not the annotate function did its job? e.g. the equivalent to > x <- readPlateList("Platelist.txt", path=datadir, name="KcViabSmall") KcViabSmall: found data in 16 x 24 (384 well) format. Read 6 plate ...
written 4.4 years ago by Joseph Barry160
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Answer: A: converting UniProt to SGD ids using UniProt.wd
... On a related note, I found somewhat strange NA behaviour. If one includes "ENSEMBL" in the "columns" vector, which returns NA, all other columns also switch to NA when returned. I guess this is not desirable behaviour for most users. > taxId(UniProt.ws) <- 559292 > species(UniProt.ws) [1] ...
written 4.9 years ago by Joseph Barry160
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Answer: A: converting UniProt to SGD ids using UniProt.wd
... Hi James, Great, thanks a lot. Works like a charm now. Best, Joseph ...
written 4.9 years ago by Joseph Barry160
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converting UniProt to SGD ids using UniProt.wd
... I would like to use UniProt.ws to convert UniProt ids to SGD ids for Saccharomyces cerevisiae but my attempts so far have resulted in the error: Error in .select(x, keys, columns, keytype) : No data is available for the keys provided. Here is a minimal example, where I attempt to convert "I2HB5 ...
uniprot.ws ensembl uniprot written 4.9 years ago by Joseph Barry160 • updated 4.9 years ago by Marc Carlson7.2k
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Answer: A: Taking out a plate from a HTS analysis
... Yes you can use the screenLog file to exclude plates. You cannot use regular expressions for this as for the plateConf file however, but you can automatically generate one with the following or similar: library(cellHTS2) myScreenLog <- data.frame(Plate=rep(4, 1536), Well=convertWellCoordinat ...
written 5.3 years ago by Joseph Barry160
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Answer: A: Plate config for 1536 plate into cellHTS2
... Dear Rossella, Your plateConf looks pretty good. You can make it a bit more concise with the following: * ^[A-H]0[1-3] RF_NoTGFB * ^[A-H]0[4-8] RF_TGFB * ^A[C-F]0[1-3] UBB_NoTGFB * ^A[C-F]0[4-8] UBB_TGFB The ^ is important to avoid any confused matches between e. ...
written 5.3 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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