User: James F. Reid

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James F. Reid610
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Posts by James F. Reid

<prev • 60 results • page 1 of 6 • next >
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Answer: A: error in hclust function
... Hi Alyaa, you probably have missing values (see 'NA/NaN/Inf in foreign function call (arg 11)') in your bb matrix. HTH. J. On 02/06/12 13:57, Alyaa Mahmoud wrote: > Hi All > > I am trying to cluster 57 COGs in 24 datasets. I use the following code and > run into this error: > > ...
written 5.5 years ago by James F. Reid610
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Answer: A: error under "hclust" for expression data
... Hi Li, check your data matrix, it looks like it might contain non-numeric data (from the NAs introduced by coercion warning). Try running a 'summary', ploting etc. Best. J. On 15/05/12 23:51, Wang, Li wrote: > Dear List Members > > I am confronted with an error when doing hierarchical cl ...
written 5.5 years ago by James F. Reid610
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Answer: A: all miRNAs related to a specific keyword, such as glioblastoma
... Hi Ali, not in BioC AFAIK. Try these web tools: miRWalk PhenomiR HTH. J. On 05/04/12 09:01, Cytochalasin wrote: > Dear all, > > Is there any package that could help in identifying all miRNAs related > to a specific keyword, such as glioblastoma? (Any other webtool/ > sofware ...
written 5.6 years ago by James F. Reid610
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Comment: C: eset from GEOqury pkg
... Hi, I should rectify that I used the GSE approach (ie getGEO("GSE2773")) and everything is fine whereas I have just checked again using the GDS approach (ie x = getGEO("GDS2248"); y = GDS2eSet(x)) and it does indeed return just numbered fvarLabels as you stated. Best. J. On 22/03/12 09:45, James ...
written 5.7 years ago by James F. Reid610
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Answer: A: eset from GEOqury pkg
... Hi, I cannot replicate this with the current version of R/BioC and with the devel one (to be released very soon), i.e I always get the fvarLabels (like in your 'old' scenario). You didn't provide a sessionInfo() so I do not know what you are using and cannot help more. J. On 21/03/12 22:43, Jing ...
written 5.7 years ago by James F. Reid610
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Biobase typo in example of AnnotatedDataFrame man page
... Dear BioC, answering to a recent query on the mailing list I noticed a small typo in the example provided in the AnnotatedDataFrame help page: AnnotatedDataFrame(data=df, varMetaData=metaData) should be AnnotatedDataFrame(data=df, varMetadata=metaData) also, no error is given when calling directl ...
written 5.7 years ago by James F. Reid610 • updated 5.7 years ago by Martin Morgan ♦♦ 20k
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Answer: A: Difficulty in AnnotatedDataFrame
... Hi Deepak, please keep the thread on the list for other users. On 02/03/12 10:28, Deepak Datta wrote: > hey James, i have read the help page and i did not find it helpful. i > would really appreciate if you could please explain me with an example > giving details on creating a metaData ...
written 5.7 years ago by James F. Reid610
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Answer: A: Difficulty in AnnotatedDataFrame
... Hi Deepak, you need to construct an AnnotatedDataFrame in the following way: AnnotatedDataFrame(data=df, varMetaData=metaData) Look-up the help page which is well documented: help("AnnotatedDataFrame") HTH. J. On 02/03/12 10:11, Deepak Datta wrote: > hii... this is Deepak.... > > i am wo ...
written 5.7 years ago by James F. Reid610
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Answer: A: getGEO error?
... Hi Hendrick, On 29/02/12 06:46, Hendrik Falk wrote: > Hi list, > > I'm trying to analyse GeneExpressionOmnibus data using the Biobase package. For the > GSE record GSE4922 I get an error as shown below, whereas other records (e.g. > GSE1456) load without problems. Is there an easy w ...
written 5.7 years ago by James F. Reid610
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Answer: A: miRNA- KEGG
... Dear Ali, here is the outline on how to do this using the miRNA predicted conserved targets using targetscan in Human (it can also be done in Mouse). myMir <- "hsa-mir-17" # 1. to find targets we need to use the mature form of the mirna # we can do this using 'mirbase.db' require("mirbase.db" ...
written 5.7 years ago by James F. Reid610

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