User: Tom
Tom • 30
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... Thanks, that's strange, on either a work server, or on my home mac laptop (no server); when I type:
efetch -db pubmed -id 24670762 -format xml
I can see XML output.
When I type:
efetch -db pubmed -id 24670762 -format xml | xtract
It says (as expected) "No command-line arguments suppl ...
written 3.7 years ago by
Tom • 30
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... I really appreciate the help.
Unfortunately, when I type:
efetch -db pubmed -id 24670762 -format xml | xtract -pattern PubmedArticle -element MedlineCitation/PMID
or
efetch -db pubmed -id 24670762 -format xml | xtract -pattern PubmedArticle -element MedlineCitation/PMID -block A ...
written 3.7 years ago by
Tom • 30
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... Hi all, I have say 100 data set names from GEO, and for each, I want to pull out a reference using Efetch.
so for example, for the list:
GDS5204
GDS520
GDS4925
The output should be:
GDS4925 D'Souza M, Zhu X, Frisina RD. Novel approach to select genes from RMA normalized microar ...
written 3.7 years ago by
Tom • 30
• updated
3.7 years ago by
Santosh Anand ♦ 5.2k
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... because it's a combination of a couple of three different data sets (i.e. two brain parts and blood) that are comparable. Thank you for the help, I appreciate it. ...
written 3.8 years ago by
Tom • 30
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... I appreciate the help, but maybe the answer is not as trivial as I thought, i've just found [this][1], so maybe using PCA with explicitly defined missing data is not possible, and I have to somehow impute the data.
[1]: http://stats.stackexchange.com/questions/35561/imputation-of-missing-values ...
written 3.8 years ago by
Tom • 30
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... So I suppose I'm wondering if there's a PCA package in either python or R, where I can read in the above table, and then there's a parameter that says something like "set missing data to NA"", and then before inputting my table into the package, I would just change all the "-" to NA. ...
written 3.8 years ago by
Tom • 30
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... The numbers are log2 transformed microarray data (actually in this example I just want to show people what I mean so the numbers are made up), but I can't set them to 0, since maybe there is a high expression for that gene, I just don't have the info for it? ...
written 3.8 years ago by
Tom • 30
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Combining gene expression data into a principal components analysis - how to deal with missing data?
... Hi all,
I have gene expression for say 9 different samples, all the same age, for say 3 different tissues (see table below, I have three samples from hippocampus, three from cerebellum and three from blood). I want to put these into a PCA plot to see if the gene expression for similar tissues clump ...
written 3.8 years ago by
Tom • 30
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... Thank you. I'm just doing a basic analysis now, and then will get into batch effects. Regarding this method, I have a few data sets for different species to check, some are as described as above, but then some, instead of each individual being a different age, there are groups of ages (e.g. I have 5 ...
written 3.9 years ago by
Tom • 30
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... Hi all,
I have a matrix; on the x axis is samples of say 100 humans of different ages, on the y axis is genes, and the cells in the matrix are log transformed microarray gene expression values.
For example:
Age20 Age21 Age30 Age40 ........-> Age90
Gene1 ...
written 3.9 years ago by
Tom • 30
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