User: Tom

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Tom30
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Posts by Tom

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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... 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 Tom30
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... 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 Tom30
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Extract Bibliographic Reference from GEO dataset using EFetch?
... 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 ...
geo ncbi efetch written 3.7 years ago by Tom30 • updated 3.7 years ago by Santosh Anand5.2k
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Comment: C: Combining gene expression data into a principal components analysis - how to dea
... 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 Tom30
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Comment: C: Combining gene expression data into a principal components analysis - how to dea
... 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 Tom30
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Comment: C: Combining gene expression data into a principal components analysis - how to dea
... 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 Tom30
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Comment: C: Combining gene expression data into a principal components analysis - how to dea
... 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 Tom30
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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 ...
R missing data gene expression pca written 3.8 years ago by Tom30
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Comment: C: Differential expression using microarray data and limma, where am I going wrong?
... 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 Tom30
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Differential expression using microarray data and limma, where am I going wrong?
... 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 ...
limma differential expression microarray written 3.9 years ago by Tom30

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Supporter 13 months ago, voted at least 25 times.
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Popular Question 3.2 years ago, created a question with more than 1,000 views. For Gene expression meta-analysis: How to correctly compile a data set.
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Popular Question 3.2 years ago, created a question with more than 1,000 views. For Convert read counts to RPKM or TPM values: Numbers don't look right?

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