Microarray analysis in R - target.txt,file,Sample info

Question

[bioinformatics]

Hi everyone,

This might be a very simple question. I'm following this microarray workflow- https://www.semel.ucla.edu/sites/default/files/coppola-lab/CoppolaExampleCode.pdf. These are the R codes I have done so far.

Microarray.MSCs <- read.delim("/Volumes/EDEN/phd/Microarray MSCs.txt", header=FALSE)

dim(Microarray.MSCs)
[1] 32408    14

head(Microarray.MSCs)

           V1        V2        V3        V4        V5        V6       V7        V8        V9
1    ProbeName   Day 0-1   Day 0-2   Day 0-3   Day 7-1   Day 7-2  Day 7-3  Day 14-1  Day 14-2
2 A_04_P063001   666.636 1696.1885  1557.941  6252.668 2919.4412 5536.268 12564.507 10459.793
3 A_04_P027222 134.40279  163.9967 150.52025  1936.827  583.9774 1742.507 1738.8904 1738.4939
4 A_04_P054052  79.53051 149.24582 276.84015 351.02386 332.94275  482.743  406.8957  289.9612
5 A_04_P043272 4.9999995  7.891682  20.59979  66.30415 57.350246 65.05819 46.807858  47.90688
6 A_04_P082033 4.9999995  5.562969  22.03437 28.541346  21.72589 45.44614 22.657038 9.8729105
        V10       V11       V12       V13          V14
1  Day 14-3  Day 21-1  Day 21-2  Day 21-3   GeneSymbol
2 10751.576   7159.59   5940.33  6241.056 LOC100346751
3 1691.0352 899.52216  653.9722  702.0644
4 411.41324 154.12201 126.39794 397.99387
5 45.024284 29.569155 26.168947  69.53682 LOC100342109
6 16.986622 7.7133107 4.9999995   57.2613

It says that I now need to read in the sample info on page 2. This is stored in the targets.txt file however I only have one file of data, an excel spreadsheet that I converted into a txt file. Does anyone know what this means or how I might make one.

Also does anyone know how to remove the non-numeric-alike variable(s) in data frame: V2, V3, V4, V5, V6, V7, V8, V9, V10, V11, V12, V13.

Thank you!

[Hyper_Odin]

• You have to copy the Table 1 (Page 3) and make a tab separated text file.

• The non-numeric data looks like header, You can remove them using

  names(Microarray.MSCs) <- NULL

[bioinformatics]

Thankyou for your help. I'm not sure what you mean. Do I create a seperate table (text file) using ProbeName and GeneSymbol columns?

[bioinformatics]

Also it removed the V1,V2,V3,V4 etc. but it still comes up with Error in Math.data.frame(Microarray.MSCs) : non-numeric-alike variable(s) in data frame: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14

thankyou

[bioinformatics]

I just have another question, is Microarray.MSCs equivalent to the data file mydataRAW in the workflow? Also what is the signal column (mentioned on page 2)? And in the workflow on page 2 what does the 8 and 2 signify in the r code mydata<-mydataRAW[,seq(1,(nsampl*8),8)+2]

Sorry for all the questions

[Hyper_Odin]

I am sorry, but you need to brush up your basics. Such as what is metadata, what is signal in microarray , genotypes, treatment e.t.c. Whatever you have asked here is well explained in the document.

[bioinformatics]

Thankyou for your response, sorry I'm new to bioinformatics and am struggling to understand.

[bioinformatics]

If it could be possible for you to explain it would be so appreciated! Thankyou

[Hyper_Odin]

You can start with this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2772365/

[bioinformatics]

Ok, thanks!