Question: NGS data analysis
0
gravatar for CancerGuy
5 weeks ago by
CancerGuy0
CancerGuy0 wrote:

I have three different excel files from three biological replicates with fold change values (transcriptome analysis). I want to combine all the data in one file, but the problem is the sequence of gene listing in file is different in all three files (eg. gene A is on 1st place in first file but is on 157th and 3045th place in file 2 and 3, respectively). This makes simple copy-paste impossible. Is there any other way to arrange this data? Thanks in advance.

rna-seq excel gene • 254 views
ADD COMMENTlink modified 5 weeks ago by AB60 • written 5 weeks ago by CancerGuy0

Are those columns sorted by the fold change values? Should it not be simple enough to re-sort the data using the gene name column and then combine the data columns in a new file/workbook?

ADD REPLYlink written 5 weeks ago by genomax28k

Some genes are missing in one or other file (due to zero read, i guess), and i have whole transcriptome there. Even after arranging gene name column i found data was not aligned correctly.

ADD REPLYlink written 5 weeks ago by CancerGuy0
3

You may be able to use join (https://unix.stackexchange.com/questions/102298/join-two-files-with-different-number-of-columns-and-rows), VLOOKUP in excel or do this in R.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by genomax28k
2

Join is good. Merge() in R also works quite well for this kind of thing:

 merge(x, y, by.x='gene' by.y = 'gene', all =T)
ADD REPLYlink written 5 weeks ago by Jacob Warner290

I'll try your suggestions. Cheers.

ADD REPLYlink written 5 weeks ago by CancerGuy0

'vlookup' in MS Excel might work for you.

ADD REPLYlink written 5 weeks ago by mbk0asis200
1
gravatar for AB
5 weeks ago by
AB60
United States
AB60 wrote:

You can use dplyr and join them.

If you want to retain all the rows in both datasets, use full join

full_join(x,y,by=c('gene.x'='gene.y')

You can use inner_join, left_join or right_join depending on whatver you want.

ADD COMMENTlink written 5 weeks ago by AB60

Awesome! That's what I was looking for.

ADD REPLYlink written 4 weeks ago by CancerGuy0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 938 users visited in the last hour