hello perlbird and welcome to the monastery!

I do not know what reshape2 has to offer, but your immediate request would be a fairly simple data manipulation exercise. Along with examples in previous reply.

#!usr/bin/perl

use warnings;
use strict;

my %genetable;

while(<DATA>){
chomp;
next if /^#/;
my ($genekey, $samplevalue ) = split /\t/;
push @{ $genetable{$genekey} }, $samplevalue;
}

print map { "$_ @{$genetable{$_}}\n" } sort keys %genetable;

exit 0;
__END__
#omitted the header row
gene_A    sample_1
gene_B    sample_1
gene_C    sample_1
gene_B    sample_2
gene_C    sample_2
gene_A    sample_3
[download]

--------
gene_A sample_1 sample_3
gene_B sample_1 sample_2
gene_C sample_1 sample_2
[download]

Yeah, see reformatting tab delimited file (and others) and Use Text::CSV or Text::xSV

Examples at

• join - join two files according to a common key
• part - split up files according to column value
• Merge two files with similar column entries
• Opening multiple files ( csvpaste.pl )
• Open multiple file handles?
• X, Y Table structure
• How to extract the particular residues from PDB files(text csv split hash bioperl)
• Select only desired features from a text (text csv split hash bioperl)
• Sort on Table headers (text csv split hash bioperl)
• I need help joining tab-delimited files/tables!
• split then join based on common value in field
• Smart way to read a file vertically?
• reformatting tab delimited file
• edit a CSV and "in-place" replacement
• Re: Reversing a mysql table, transpose-tsv -- invert a tab-delimited table

• Text::CSV

  examples/csv2xls	Script to onvert CSV files to M$Excel
  examples/csv-check	Script to check a CSV file/stream
  examples/csvdiff	Script to shoff diff between sorted CSV files
  examples/parser-xs.pl	Parse CSV stream, be forgiving on bad lines

 [CSV hash ] CSV hash

Best way to match a hash with large CSV file

perl hash to CSV using Text::CSV_XS

Issue parsing CSV into hashes?

Veriable Length Array/Hash derived from CSV to populate an XML

extracting data from CSV files and making hash of hashes

Re^2: build hash from csv file

Encoding a hash in perl before saving it as a CSV file

hash from CSV-like structure

Read the csv file to a hash....

Parsing CSV into a hash

build hash from csv file

Converting a CSV list to a list of hashrefs naming the fields

By what sort of decision chain/data testing do we get to an output for  gene a.... that includes   gene_A sample_2 when there is no  gene_A sample_2 in the original data? I infer that it is not because the original data has two  geneA... entities because the  geneC sample...< /c> data do <b>NOT>/b> include 3 distinct data points to justify the<c> gene_C sample_3 output.

Minor update, mostly to offset data citations more clearly

please reformat your posting:

• <p> between paragraphs
• <c> ... </c> around code and data
• [ ... ] around links

use strict;
use warnings;
my %result;                             # Hash of Arrays

my $headline = <DATA>;                         # ignore
while (my $line =<DATA>) {
  my ($gene,$sample) = split /\s+/, $line;
  push @{$result{$gene}},$sample;
}

for my $gene (sort keys %result) {
  print join "\t", $gene, @{$result{$gene}};
  print "\n";
}

__DATA__
Gene_name sample
gene_A    sample_1
gene_B    sample_1
gene_C    sample_1
gene_B    sample_2
gene_C    sample_2
gene_A    sample_3
[download]

-->

gene_A    sample_1    sample_3
gene_B    sample_1    sample_2
gene_C    sample_1    sample_2
[download]

wow. that's really neat and handy!

Thanks Rolf!!