User: english.server

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Posts by english.server

<prev • 10 results • page 1 of 1 • next >
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Comment: C: How to check whether experimental covariates are confounded with our group of in
... Thank you for your response. I think I've to study a little more to digest the concept. ...
written 9 weeks ago by english.server20
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Comment: C: How to check whether experimental covariates are confounded with our group of in
... Thank you Gordon Smyth. Regarding my previous post, I *thought* the concepts asked there are different from what is asked here! Thanks for clarification. You are absolutely right about me wanting to "analyse microarray datasets automatically without having to look at plots or think about the variabl ...
written 9 weeks ago by english.server20
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How to check whether experimental covariates are confounded with our group of interest?
... Hi In the context of microarray analysis, how to check whether experimental covariates (age/gender) are confounded with our grouping of interest (ie diseased vs normal)? goi = sample(letters[1:2], 20, T) # group of interest cov=list() #3 covariates cov$c1=sample(letters[1:4], 20 ...
microarray covariates written 10 weeks ago by english.server20
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Comment: C: Limma DEG analysis experiment with partial paired design + batch effect
... Great response, and thank you again for your detailed response. I think I got the main ideas. ...
written 11 weeks ago by english.server20
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Comment: C: Limma DEG analysis experiment with partial paired design + batch effect
... Thank you @Gordon Smyth for your analytic response. In geneal, how should one *check* whether factors are confounded? On googling I ended up with chisq.test(). However, chisq.test(a$batch, a$donor) #p-value = 0.2867 chisq.test(a$pair , a$donor) #p-value = 0.01 chisq.test(a$co ...
written 11 weeks ago by english.server20
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Comment: C: Limma DEG analysis experiment with partial paired design + batch effect
... Thank you. I updated the original question according to your post. PS. I also edited the title. ...
written 11 weeks ago by english.server20
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Limma DEG analysis experiment with partial paired design + batch effect
... Hi! While re-analyzing GSE65106 from GEO, I have constructed a table containing a subset of samples, as follows: > a # see below for dput(a) accession cond donor batch pair A1.r1 GSM1587362 ASD AA1 1a 1 A1.r2 GSM1587363 ASD AA1 2a 1 A2.r1 ...
limma paired batch written 11 weeks ago by english.server20 • updated 11 weeks ago by Gordon Smyth39k
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Comment: C: affymetrix miRNA microarray analysis, (package mirna30cdf)
... Thank you indeed very much. ...
written 20 months ago by english.server20
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affymetrix miRNA microarray analysis, (package mirna30cdf)
... Hi every one! miRNA 3.0 CDF Library File  is present at affymetrix site However, while I want to use affy (not oligo) for analysis of this type of array, I get the error that mirna30cdf not available. Any help would be appreciated. ...
microarray affy written 20 months ago by english.server20 • updated 20 months ago by James W. MacDonald52k
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Reading in .gpr files
... Hi everyone!   I need to read in .gpr files downloaded from GEO. I cant get either read.maimages {limma} or read.GenePix {marray} working. Where am I wrong? Thank you inn advance. files= dir() files= files [grep(files, pattern = '*.gpr$')] library (limma) #1 library (marray) #2 data= read.maim ...
microarray written 21 months ago by english.server20 • updated 21 months ago by Gordon Smyth39k

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