User: maxininfa

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maxininfa0
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Posts by maxininfa

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Comment: C: SPIA plotP giving error
... I have the same problem/question. Looking at the code: https://rdrr.io/bioc/SPIA/src/R/plotP.R if(threshold ...
written 6 months ago by maxininfa0
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Comment: C: aafTableAnn complaining about NAs when there are none
... Thank you very much! ...
written 6 months ago by maxininfa0
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aafTableAnn complaining about NAs when there are none
... Hi! I'm following this [guide][1] to analyze the raw data from this study (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18670/). I arrived at the "11.4 Adding more annotation" part, and tried running: > anncols <- aaf.handler()[c(1:2,9:12)] > atab <- aafTableAnn(T2$sym ...
microarray hgu133plus2.db aaftableann annafy written 6 months ago by maxininfa0 • updated 6 months ago by James W. MacDonald50k
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Comment: C: lm.fit incompatible dimensions
... OMG, I feel so stupid now xD Thanks!!! ...
written 6 months ago by maxininfa0
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lm.fit incompatible dimensions
... Hi! I'm trying to follow this [guide][1] to analyze this [raw ArrayExpress data][2] and I'm stucked really hard at the [Identification of DE genes][3] with the "Three groups of samples" example. Personally the data has 4 groups, but it should be the same up to this point. > f [1] tumo ...
limma oligo arrayexpress written 6 months ago by maxininfa0 • updated 6 months ago by James W. MacDonald50k
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Comment: C: Could not access the Bioconductor repository
... Thx! I did install it, the sad part is that ArrayExpress isn't supported on 3.5. I hope I can install 3.4 in parallel and access the package. ...
written 6 months ago by maxininfa0
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Could not access the Bioconductor repository
... Hi! I'm following the ArrayExpress [vignette][1] to analyze an experiment, but can't follow through when I need to download the annotation package pd.hg.u133.plus.2 > library(oligo) > data = read.celfiles(list) Loading required package: pd.hg.u133.plus.2 Attempting to obtain ' ...
arrayexpress bioconductor proxy written 6 months ago by maxininfa0 • updated 6 months ago by James W. MacDonald50k
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Comment: C: DGE matrix annotation
... Hi James! 1) I didn't know that there was such a restricted way to do things regarding this data, thank you for pointing it out. 2) I think I have this particulars versions because there are some packages that arent supported in newer versions (now I can't remember which, but it truly rings a bell ...
written 9 months ago by maxininfa0
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DGE matrix annotation
... Hi everyone! I'm trying to apply pathway analysis to Array Express experiments. For that I downloaded the processed data, along with the sample and data relationship files (e.g. https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15641/). I made every value an integer (I know this isn't how the p ...
annotationdbi deseq2 dge written 9 months ago by maxininfa0 • updated 9 months ago by James W. MacDonald50k

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