User: Biologist

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Biologist90
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Posts by Biologist

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Comment: C: Differential analysis with microarray data without idat or cel files
... Thank you very much Kevin. A small help. In the above data in my question the how can I convert those probes to gene symbols? ...
written 10 hours ago by Biologist90
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Comment: C: Differential analysis with microarray data without idat or cel files
... Yes, when I downloaded that `GSE60689_RAW.tar` file the above data is what I see, that is what I said in my previous comment. ...
written 11 hours ago by Biologist90
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Comment: C: Differential analysis with microarray data without idat or cel files
... I didn't find any tar.gz file for that. I have seen all the links related to that data. ...
written 12 hours ago by Biologist90
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Comment: C: Differential analysis with microarray data without idat or cel files
... What they say here [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60689] is that data is processed by Arraystar Human LncRNA Array v3.0. I have seen all the links but nowhere I found that raw file for the data. The above data is what I have now. ...
written 12 hours ago by Biologist90
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Comment: C: Differential analysis with microarray data without idat or cel files
... Sure will have a look. Now with this data how can I go for differential analysis. Bit confused with the Lima user guide. can you please give some example code for the differential analysis with the above data. thanq ...
written 12 hours ago by Biologist90
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Comment: C: Differential analysis with microarray data without idat or cel files
... Hi Kevin, I log transformed the data and using quantile normalisation and made a box plot. I see that distribution looks fine. data <- read.csv("MicroarrayData.csv") data2 <- data.frame(data[,-1], row.names=data[,1]) data3 <- log2(as.matrix(data2)) data4 <- normali ...
written 12 hours ago by Biologist90
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Comment: C: Differential analysis with microarray data without idat or cel files
... I don't see any cel or idat files. I see a Raw_tar file for each sample. For one of the sample it looks like below. ProbeName PositionX PositionY gProcessedSignal gProcessedSigError gMedianSignal gBGMedianSignal gBGPixSDev gBGSubSignal gIsPosAndSignif gIsWellAboveBG SpotExtentX gBGMeanSignal ...
written 12 hours ago by Biologist90
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Differential analysis with microarray data without idat or cel files
... Hi, I have downloaded LncRNA Array 3.0 (ArrayStar) microarray data from GEO. The data is in `txt` format. I don't see any idat or cel files for analysis with Limma or other Bioconductor packages. The data looks like this. ID_REF GSM1485226 GSM1485227 GSM1485228 GSM1485229 ASHGA5P00 ...
differential analysis R gene expression microarray written 13 hours ago by Biologist90 • updated 12 hours ago by Kevin Blighe32k
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Comment: C: Where Can I find protein-protein interactions data ?
... Thanks a lot for the link. ...
written 4 days ago by Biologist90
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Comment: C: Where Can I find protein-protein interactions data ?
... Thank you very much ...
written 4 days ago by Biologist90

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